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Variant Annotations

Cases are processed via the bioinformatics pipeline and additional annotations are added by Cellbase. Once a case arrives to the DSS, additional annotations are added from resources that are currently unavailable in Cellbase.

Annotation Description Source
gnomAD (exomes) Population Germline Allele Frequency Database Cellbase
Ensembl Transcript and Protein ID annotations Cellbase
RefSeq Transcript annotations Cellbase
ClinVar Germline Database Cellbase
NGTD NHS resource DSS
PanelApp GEL resource DSS
SV Frequencies GEL dataset DSS
CGC annotations Somatic Database DSS
Cancer Hotspots Somatic Database DSS
SVIG canonical variant list Somatic Database DSS
GEL 100K somatic frequencies GEL dataset DSS

Info

Please note that COSMIC annotations have been removed from the DSS from release 6.18.0 onwards due to licensing changes. Please see Release notes for further details.

The Genome Aggregation Database (gnomAD) is a population frequency database of large-scale sequencing projects from healthy cohorts.

  • Cellbase annotates whether a variant is present in the gnomAD exomes dataset.
  • The DSS displays the total population germline allele frequency as well as the alternate allele frequency, alternate allele count, allele number, and number of individuals homozygous for the alternate allele in each subpopulation.
  • The database version of gnomAD used by Cellbase is displayed in the DSS and may not always be the most recent. Please see the latest version of the Cancer Genome Analysis guide and Cellbase for further details.

The Cancer Hotspots Database consists of single residue and in-frame indel mutation hotspots identified in 24,592 tumor samples by the algorithm described in Chang et al. 2017 and Chang et al. 2016, as well as 164 hotspots reported in Bandlamudi et al., 2026.

Warning

Cancer hotspot annotations have not been updated to contain the latest 164 hotspots reported in Bandlamudi et al., 2026

  • If the variant is located in a hotspot identified by Cancer Hotspots, the cancer hotspots icon will show in the database column in the variant grid.
  • We currently match hotspots using the ensembl protein ID. Cancerhotspots.org have used Ensembl v75, while our pipeline uses MANE transcripts. Please see below for a comparison between all protein IDs.
  • In cases where the protein ID does not match, we will not detect a hotspot in that gene. We recommend navigating to the cancerhotspots.org database via the linkout provided and manually searching for the hotspot, then comparing protein sequences to ensure the protein sequence matches at that position.
Proteins
HGNC Symbol Ensembl 75 Ensembl 90 MANE Notes
ACVR1 ENSP00000263640 ENSP00000263640 ENSP00000405004.1
AKT1 ENSP00000270202 ENSP00000450688 ENSP00000497822.1
AKT3 ENSP00000263826 ENSP00000336943 ENSP00000500582.1
ALK ENSP00000373700 ENSP00000373700 ENSP00000373700.3
ANKRD11 ENSP00000301030 ENSP00000367581 ENSP00000301030.4
APC ENSP00000257430 ENSP00000257430 ENSP00000257430.4
AR ENSP00000363822 ENSP00000363822 ENSP00000363822.3
ARAF ENSP00000366244 ENSP00000366244 ENSP00000366244.4
ARID1A ENSP00000320485 ENSP00000320485 ENSP00000320485.7
ARID1B ENSP00000344546 ENSP00000344546 ENSP00000490491.2
ARID2 ENSP00000335044 ENSP00000335044 ENSP00000335044.6
ASXL2 ENSP00000391447 ENSP00000391447 ENSP00000391447.3
ATM ENSP00000278616 ENSP00000278616 ENSP00000501606.1
ATRX ENSP00000362441 ENSP00000362441 ENSP00000362441.4
AXIN1 ENSP00000262320 ENSP00000262320 ENSP00000262320.3
AXL ENSP00000301178 ENSP00000301178 ENSP00000301178.3
B2M ENSP00000452780 ENSP00000452780 ENSP00000497910.1
BCL10 ENSP00000359612 ENSP00000359612 ENSP00000498104.1
BCL2 ENSP00000329623 ENSP00000381185 ENSP00000329623.3
BCL2L11 ENSP00000376943 ENSP00000482175 ENSP00000376943.2
BCL6 ENSP00000232014 ENSP00000384371 ENSP00000384371.2
BCOR ENSP00000367705 ENSP00000367705 ENSP00000367705.4
BRAF ENSP00000288602 ENSP00000288602 ENSP00000496776.1
BRCA2 ENSP00000369497 ENSP00000439902 ENSP00000369497.3
BRD4 ENSP00000263377 ENSP00000263377 ENSP00000506350.1
CARD11 ENSP00000380150 ENSP00000380150 ENSP00000380150.4
CASP8 ENSP00000351273 ENSP00000264275 ENSP00000501268.1
CBFB ENSP00000415151 ENSP00000415151 ENSP00000415151.2
CBL ENSP00000264033 ENSP00000264033 ENSP00000264033.3
CCND1 ENSP00000227507 ENSP00000227507 ENSP00000227507.2
CCND3 ENSP00000362082 ENSP00000362082 ENSP00000362082.5
CD79B ENSP00000376544 ENSP00000376544 ENSP00000006750.4
CDH1 ENSP00000261769 ENSP00000261769 ENSP00000261769.4
CDK12 ENSP00000398880 ENSP00000398880 ENSP00000398880.4
CDK4 ENSP00000257904 ENSP00000257904 ENSP00000257904.5
CDK6 ENSP00000265734 ENSP00000265734 ENSP00000397087.3
CDKN1A ENSP00000244741 ENSP00000409259 ENSP00000244741.6
CDKN1B ENSP00000228872 ENSP00000228872 ENSP00000228872.4
CDKN2A ENSP00000307101 ENSP00000307101 ENSP00000307101.5
CHEK2 ENSP00000329178 ENSP00000329178 ENSP00000385747.1
CIC ENSP00000458663 ENSP00000458663 ENSP00000505728.1
CREBBP ENSP00000262367 ENSP00000262367 ENSP00000262367.5
CRLF2 ENSP00000370978 ENSP00000383641 ENSP00000383641.3
CTCF ENSP00000264010 ENSP00000264010 ENSP00000264010.4
CTLA4 ENSP00000303939 ENSP00000303939 ENSP00000497102.1
CTNNB1 ENSP00000344456 ENSP00000344456 ENSP00000344456.5
CUL3 ENSP00000264414 ENSP00000264414 ENSP00000264414.4
CYSLTR2 ENSP00000282018 ENSP00000282018 ENSP00000508181.1
DICER1 ENSP00000343745 ENSP00000343745 ENSP00000343745.3
DIS3 ENSP00000366997 ENSP00000366997 ENSP00000366997.4
DNAJB1 ENSP00000254322 ENSP00000254322 ENSP00000254322.1
DNMT1 ENSP00000345739 ENSP00000352516 ENSP00000352516.3
DNMT3A ENSP00000264709 ENSP00000324375 ENSP00000324375.5
DNMT3B ENSP00000328547 ENSP00000328547 ENSP00000328547.2
EGFR ENSP00000275493 ENSP00000275493 ENSP00000275493.2
EIF1AX ENSP00000368927 ENSP00000368927 ENSP00000368927.5
EIF4A2 ENSP00000326381 ENSP00000326381 ENSP00000326381.5
EP300 ENSP00000263253 ENSP00000263253 ENSP00000263253.7
EPAS1 ENSP00000263734 ENSP00000263734 ENSP00000263734.3
EPHA3 ENSP00000337451 ENSP00000337451 ENSP00000337451.2
EPHA7 ENSP00000358309 ENSP00000358309 ENSP00000358309.4
EPHB1 ENSP00000381097 ENSP00000381097 ENSP00000381097.3
ERBB2 ENSP00000269571 ENSP00000269571 ENSP00000269571.4
ERBB3 ENSP00000267101 ENSP00000267101 ENSP00000267101.4
ERBB4 ENSP00000342235 ENSP00000342235 ENSP00000342235.4
ERCC2 ENSP00000375809 ENSP00000375809 ENSP00000375809.4
ERCC3 ENSP00000285398 ENSP00000285398 ENSP00000285398.2
ERG ENSP00000288319 ENSP00000414150 ENSP00000288319.7
ERRFI1 ENSP00000366702 ENSP00000366702 ENSP00000366702.5
ESR1 ENSP00000206249 ENSP00000206249 ENSP00000206249.3
ETV6 ENSP00000379658 ENSP00000379658 ENSP00000379658.3
EZH2 ENSP00000320147 ENSP00000320147 ENSP00000320147.2
FAM58A ENSP00000384396 ENSP00000461135 ENSP00000461135.1 CCNQ in MANE
FAT1 ENSP00000406229 ENSP00000406229 ENSP00000406229.2
FBXW7 ENSP00000281708 ENSP00000281708 ENSP00000281708.3
FGFR1 ENSP00000393312 ENSP00000400162 ENSP00000400162.2
FGFR2 ENSP00000351276 ENSP00000410294 ENSP00000351276.6
FGFR3 ENSP00000260795 ENSP00000414914 ENSP00000414914.2
FGFR4 ENSP00000292408 ENSP00000292408 ENSP00000292408.4
FH ENSP00000355518 ENSP00000355518 ENSP00000355518.4
FLT3 ENSP00000241453 ENSP00000241453 ENSP00000241453.7
FOXA1 ENSP00000250448 ENSP00000250448 ENSP00000250448.3
FOXL2 ENSP00000333188 ENSP00000333188 ENSP00000497217.1
FOXO1 ENSP00000368880 ENSP00000368880 ENSP00000368880.4
FOXP1 ENSP00000318902 ENSP00000318902 ENSP00000497369.1
FUBP1 ENSP00000359804 ENSP00000359804 ENSP00000359804.2
GATA2 ENSP00000345681 ENSP00000345681 ENSP00000345681.2
GATA3 ENSP00000341619 ENSP00000368632 ENSP00000368632.3
GLI1 ENSP00000228682 ENSP00000228682 ENSP00000228682.2
GNA11 ENSP00000078429 ENSP00000078429 ENSP00000078429.3
GNAQ ENSP00000286548 ENSP00000286548 ENSP00000286548.4
GNAS ENSP00000360126 ENSP00000346328 ENSP00000360115.3
GPS2 ENSP00000370104 ENSP00000379841 ENSP00000370104.2
GSK3B ENSP00000324806 ENSP00000324806 ENSP00000264235.9
GTF2I ENSP00000322542 ENSP00000460070 ENSP00000460070.1
H3F3A ENSP00000355778 ENSP00000355780 ENSP00000355780
HGF ENSP00000222390 ENSP00000222390 ENSP00000222390.5
HIST1H1C ENSP00000339566 ENSP00000339566 ENSP00000339566.3 H1-2 in MANE
HIST1H3B ENSP00000244661 ENSP00000484841 ENSP00000484841.2 H3-C2 in MANE
HIST1H3C ENSP00000439493 ENSP00000484658 ENSP00000484658.2 H3-C3 in MANE
HIST1H3H ENSP00000358160 ENSP00000358160 ENSP00000509120.1 H3C10 in MANE
HLA-A ENSP00000366005 ENSP00000366002 ENSP00000366005.5
HLA-B ENSP00000399168 ENSP00000399168 ENSP00000399168.2
HNF1A ENSP00000257555 ENSP00000257555 ENSP00000257555.5
HRAS ENSP00000309845 ENSP00000407586 ENSP00000309845.7
IDH1 ENSP00000260985 ENSP00000260985 ENSP00000260985.2
IDH2 ENSP00000331897 ENSP00000331897 ENSP00000331897.4
IGF1R ENSP00000268035 ENSP00000268035 ENSP00000497069.1
IKZF1 ENSP00000331614 ENSP00000331614 ENSP00000331614.3
IL7R ENSP00000306157 ENSP00000306157 ENSP00000306157.3
INPPL1 ENSP00000298229 ENSP00000298229 ENSP00000298229.2
IRF4 ENSP00000370343 ENSP00000370343 ENSP00000370343.4
IRS2 ENSP00000365016 ENSP00000365016 ENSP00000365016.3
JAK1 ENSP00000343204 ENSP00000343204 ENSP00000343204.4
JUN ENSP00000360266 ENSP00000360266 ENSP00000360266.2
KDM6A ENSP00000367203 ENSP00000367203 ENSP00000483595.2
KDR ENSP00000263923 ENSP00000263923 ENSP00000263923.4
KEAP1 ENSP00000171111 ENSP00000377245 ENSP00000171111.4
KIT ENSP00000288135 ENSP00000288135 ENSP00000288135.6
KLF4 ENSP00000363804 ENSP00000363804 ENSP00000363804.4
KMT2A ENSP00000436786 ENSP00000436786 ENSP00000436786.2
KMT2C ENSP00000262189 ENSP00000262189 ENSP00000262189.6
KMT2D ENSP00000301067 ENSP00000301067 ENSP00000301067.7
KNSTRN ENSP00000249776 ENSP00000249776 ENSP00000249776.8
KRAS ENSP00000256078 ENSP00000256078 ENSP00000308495.3
LYN ENSP00000428924 ENSP00000428924 ENSP00000428924.1
MAP2K1 ENSP00000302486 ENSP00000302486 ENSP00000302486.5
MAP2K2 ENSP00000262948 ENSP00000262948 ENSP00000262948.4
MAP2K4 ENSP00000262445 ENSP00000410402 ENSP00000262445.5
MAP3K1 ENSP00000382423 ENSP00000382423 ENSP00000382423.3
MAP3K13 ENSP00000265026 ENSP00000265026 ENSP00000265026.3
MAPK1 ENSP00000215832 ENSP00000215832 ENSP00000215832.7
MAX ENSP00000351490 ENSP00000351490 ENSP00000351490.4
MED12 ENSP00000363193 ENSP00000363193 ENSP00000363193.3
MEF2B ENSP00000162023 ENSP00000402154 ENSP00000402154.2
MET ENSP00000380860 ENSP00000317272 ENSP00000380860.3
MGA ENSP00000219905 ENSP00000219905 N/A non-coding in MANE
MSH2 ENSP00000233146 ENSP00000233146 ENSP00000233146.2
MST1 ENSP00000414287 ENSP00000414287 ENSP00000414287.2
MTOR ENSP00000354558 ENSP00000354558 ENSP00000354558.4
MYC ENSP00000367207 ENSP00000479618 ENSP00000478887.2
MYCN ENSP00000281043 ENSP00000281043 ENSP00000281043.3
MYD88 ENSP00000379625 ENSP00000379625 ENSP00000498360.2
MYOD1 ENSP00000250003 ENSP00000250003 ENSP00000250003.3
NCOA3 ENSP00000361066 ENSP00000361066 ENSP00000361066.3
NF1 ENSP00000351015 ENSP00000351015 ENSP00000351015.4
NFE2L2 ENSP00000380252 ENSP00000380252 ENSP00000380252.3
NOTCH1 ENSP00000277541 ENSP00000277541 ENSP00000498587.1
NOTCH2 ENSP00000256646 ENSP00000256646 ENSP00000256646.2
NRAS ENSP00000358548 ENSP00000358548 ENSP00000358548.4
NSD1 ENSP00000395929 ENSP00000395929 ENSP00000395929.2
NUP93 ENSP00000310668 ENSP00000310668 ENSP00000310668.5
PAK7 ENSP00000322957 ENSP00000367686 ENSP00000322957.5 PAK5 in MANE
PARP1 ENSP00000355759 ENSP00000355759 ENSP00000355759.5
PAX5 ENSP00000350844 ENSP00000350844 ENSP00000350844.4
PBRM1 ENSP00000378307 ENSP00000378307 N/A Pending MANE review
PDGFRA ENSP00000257290 ENSP00000257290 ENSP00000257290.5
PDPK1 ENSP00000344220 ENSP00000344220 ENSP00000344220.4
PGR ENSP00000325120 ENSP00000325120 ENSP00000325120.5
PIK3CA ENSP00000263967 ENSP00000263967 ENSP00000263967.3
PIK3CB ENSP00000289153 ENSP00000289153 ENSP00000501150.1
PIK3CD ENSP00000366563 ENSP00000366563 ENSP00000366563.4
PIK3R1 ENSP00000274335 ENSP00000428056 ENSP00000428056.1
PIK3R2 ENSP00000222254 ENSP00000222254 ENSP00000222254.6
PIM1 ENSP00000362608 ENSP00000362608 ENSP00000362608.5
PLK2 ENSP00000274289 ENSP00000274289 ENSP00000274289.3
PMS2 ENSP00000265849 ENSP00000265849 ENSP00000265849.7
POLE ENSP00000322570 ENSP00000322570 ENSP00000322570.5
PPM1D ENSP00000306682 ENSP00000306682 ENSP00000306682.2
PPP2R1A ENSP00000324804 ENSP00000324804 ENSP00000324804.6
PPP4R2 ENSP00000432104 ENSP00000349124 ENSP00000349124.5
PPP6C ENSP00000362648 ENSP00000392147 ENSP00000362648.4
PRDM14 ENSP00000276594 ENSP00000276594 ENSP00000276594.2
PREX2 ENSP00000288368 ENSP00000288368 ENSP00000288368.4
PRKCI ENSP00000295797 ENSP00000295797 ENSP00000295797.4
PTEN ENSP00000361021 ENSP00000361021 ENSP00000361021.3
PTPN11 ENSP00000340944 ENSP00000340944 ENSP00000340944.3
PTPRD ENSP00000348812 ENSP00000370593 ENSP00000370593.3
PTPRS ENSP00000349932 ENSP00000465185 ENSP00000262963.8
PTPRT ENSP00000362294 ENSP00000362294 ENSP00000362283.1
RAC1 ENSP00000348461 ENSP00000348461 ENSP00000258737.7
RAD50 ENSP00000265335 ENSP00000368100 ENSP00000368100.4
RAD51C ENSP00000336701 ENSP00000336701 ENSP00000336701.4
RAD52 ENSP00000351284 ENSP00000351284 ENSP00000351284.3
RAF1 ENSP00000251849 ENSP00000251849 ENSP00000251849.4
RARA ENSP00000254066 ENSP00000254066 ENSP00000254066.5
RB1 ENSP00000267163 ENSP00000267163 ENSP00000267163.4
RBM10 ENSP00000328848 ENSP00000366829 ENSP00000366829.3
RECQL4 ENSP00000475456 ENSP00000482313 ENSP00000482313.2
RET ENSP00000347942 ENSP00000347942 ENSP00000347942.3
RHEB ENSP00000262187 ENSP00000262187 ENSP00000262187.5
RHOA ENSP00000400175 ENSP00000400175 ENSP00000400175.1
RICTOR ENSP00000349959 ENSP00000349959 ENSP00000349959.3
RIT1 ENSP00000357306 ENSP00000357306 ENSP00000357306.3
RNF43 ENSP00000385328 ENSP00000462764 ENSP00000385328.2
RPS6KA4 ENSP00000333896 ENSP00000333896 ENSP00000333896.4
RPTOR ENSP00000307272 ENSP00000307272 ENSP00000307272.3
RRAS2 ENSP00000256196 ENSP00000437547 ENSP00000256196.4
RUNX1 ENSP00000300305 ENSP00000409227 ENSP00000501943.1
RXRA ENSP00000419692 ENSP00000419692 ENSP00000419692.1
SDHA ENSP00000264932 ENSP00000264932 ENSP00000264932.6
SDHAF2 ENSP00000301761 ENSP00000301761 ENSP00000301761.3
SESN2 ENSP00000253063 ENSP00000253063 ENSP00000253063.3
SETD2 ENSP00000386759 ENSP00000386759 ENSP00000386759.3
SF3B1 ENSP00000335321 ENSP00000335321 ENSP00000335321.6
SMAD2 ENSP00000262160 ENSP00000349282 ENSP00000262160.6
SMAD3 ENSP00000332973 ENSP00000332973 ENSP00000332973.4
SMAD4 ENSP00000341551 ENSP00000341551 ENSP00000341551.3
SMARCA4 ENSP00000343896 ENSP00000397783 ENSP00000343896.4
SMARCB1 ENSP00000263121 ENSP00000263121 ENSP00000494049.2
SMARCD1 ENSP00000378414 ENSP00000378414 ENSP00000378414.4
SMO ENSP00000249373 ENSP00000249373 ENSP00000249373.3
SOCS1 ENSP00000329418 ENSP00000329418 ENSP00000329418.2
SOS1 ENSP00000384675 ENSP00000384675 ENSP00000384675.2
SOX17 ENSP00000297316 ENSP00000297316 ENSP00000297316.4
SPOP ENSP00000240327 ENSP00000377001 ENSP00000425905.1
SPRED1 ENSP00000299084 ENSP00000299084 ENSP00000299084.4
SRSF2 ENSP00000353089 ENSP00000376276 ENSP00000353089.5
STAG2 ENSP00000218089 ENSP00000218089 ENSP00000360187.4
STAT3 ENSP00000264657 ENSP00000264657 ENSP00000264657.4
STK11 ENSP00000324856 ENSP00000324856 ENSP00000324856.6
STK19 ENSP00000364480 ENSP00000364482 ENSP00000509445.1
SUZ12 ENSP00000316578 ENSP00000316578 ENSP00000316578.5
TBX3 ENSP00000257566 ENSP00000257566 ENSP00000257567.2
TCEB1 ENSP00000284811 ENSP00000428171 ENSP00000428171.1 ELOC in MANE
TCF3 ENSP00000344375 ENSP00000262965 ENSP00000262965.5
TCF7L2 ENSP00000444972 ENSP00000358404 ENSP00000348274.4
TET1 ENSP00000362748 ENSP00000362748 ENSP00000362748.4
TET2 ENSP00000369351 ENSP00000369351 ENSP00000369351.4
TGFBR1 ENSP00000364133 ENSP00000364133 ENSP00000364133.4
TGFBR2 ENSP00000351905 ENSP00000351905 ENSP00000295754.5
TNFRSF14 ENSP00000347948 ENSP00000347948 ENSP00000347948.4
TP53 ENSP00000269305 ENSP00000269305 ENSP00000269305.4
TP63 ENSP00000264731 ENSP00000264731 ENSP00000264731.3
TRAF7 ENSP00000318944 ENSP00000318944 ENSP00000318944.6
TSC1 ENSP00000298552 ENSP00000298552 ENSP00000298552.3
U2AF1 ENSP00000291552 ENSP00000291552 ENSP00000291552.4
VHL ENSP00000256474 ENSP00000256474 ENSP00000256474.3
WHSC1 ENSP00000372347 ENSP00000423972 ENSP00000423972.1 NSD2 in MANE
XPO1 ENSP00000384863 ENSP00000384863 ENSP00000384863.2

Info

Cancer hotspot annotations are not currently available for splice variants or InDels, but will be in a future release. Until then, we recommend you check the cancerhotspots.org website for these variants.

We annotate variants against the SVIG canonical variant list. We display the SVIG flag in the cDSS for two scenarios:

  1. Exact match: if the exact variant is found in the SVIG canonical variant list, we display an 'SVIG' flag with the associated tooltip "This is a variant from the Somatic Variant Interpretation Guidelines (SVIG) canonical variant list"
  2. Region overlap: if the variant falls into the genomic region where an SVIG canonical variant is located, we display an 'SVIG region' flag and the associated tooltip "This is a variant falling into the genomic region where an SVIG canonical variant is located"
Match Variant Grid Tooltip
Exact match Image This is a variant from the Somatic Variant Interpretation Guidelines (SVIG) canonical variant list
Region overlap Image This is a variant falling into the genomic region where an SVIG canonical variant is located

We annotate variants against the GEL 100K somatic frequencies dataset derived from the data published by Sonsinsky et al., 2024 encompassing a total of 11,374 samples. The 100K somatic frequencies is a large, accurate and robust dataset from the UK population which is ideal for case counting. At present, the dataset contains only small non-synonymous somatic variants from solid tumours.

Variant Grid

We display the GEL 100K somatic frequencies annotation in the variant grid across three scenarios:

  1. Gene match: if the variant is annotated to a gene that was included in the GEL 100K somatic frequencies
  2. Protein match: if the variant results in a matching protein sequence change, without matching the coding sequence (nucleotide) change
  3. Coding sequence match: if the variant matches at the coding sequence (nucleotide) and protein sequence change level

Each match is represented differently in the variant grid as shown below.

Match Variant Grid Tooltip Variant Types
Gene Image Gene match present for this variant in GEL 100k somatic frequencies Domained variants
Protein match Image Protein match present for this variant in GEL 100k somatic frequencies Domained and undomained variants
Coding sequence Image No of samples in GEL 100K dataset with a coding sequence (nucleotide) change Domained and undomained variants

Database Entries Overlay

When a protein or a coding sequence match is found, the overlay includes a table where a breakdown of all the samples and cancer sample types included in the study that match the variant is shown.

The content of the overlay depends on the match and the variant type and can be accessed from the somatic small variant grid. The possible column defintions are shown below;

  1. Cancer Type - All the tumour types listed in alphabetical order
  2. CDS change - Number of samples with the searched variant resulting in the same coding sequence change
  3. Protein change - Number of samples with the searched variant resulting in the same protein change
  4. Truncating variants in this position and downstream - Counts for all truncating variants at the same position of further downstream ll
  5. In-frame deletions (within the same amino acid region) - Counts for all in-frame deletions within the same amino acid region
  6. Total number of samples - Total number of samples with that tumour type in the data set
Variant Type Match Overlay
Missense or start loss Protein
Image title
The number of samples per cancer type and across all samples included in the study with a variant resulting in the same protein change
Missense or start loss Coding sequence
Image
The number of samples per cancer type and across all samples included in the study with a variant resulting in the same coding sequence and protein change
Frameshift or stop gained Protein
Image
The number of samples per cancer type and across all samples included in the study with a variant resulting in the same protein change and sample counts for truncating variants at this position and downstream
Frameshift or stop gained Coding sequence
Image
The number of samples per cancer type and across all samples included in the study with a variant resulting in the same coding sequence and protein change and sample counts for truncating variants in this position and downstream
In-frame deletion Protein
Image
The number of samples per cancer type and across all samples included in the study with a variant resulting in the same protein change and sample counts for in-frame deletions within the same amino acid region
In-frame deletion Coding sequence
Image
The number of samples per cancer type and across all samples included in the study with a variant resulting in the same coding sequence and protein change and sample counts for in-frame deletions within the same amino acid region
Splice site variants, in-frame insertions Coding sequence
Image
The number of samples per cancer type and across all samples included in the study with a variant resulting in the same coding sequence change

Sample counts = The number of samples per cancer type and across all samples included in the study

Ensembl is a genome browser that provides gene annotations.

  • Cellbase annotates each variant with a transcript and protein ID from Ensembl.
  • The DSS displays these annotations in the variant list and variant details page.
  • The database version of Ensembl used by Cellbase may not always be the most recent. Please see the latest version of the Cancer Genome Analysis guide and Cellbase for further details.

RefSeq is a sequence annotation resource.

  • Transcripts included in the MANE project will have a RefSeq transcript ID annotation that corresponds to the Ensembl transcript ID.
  • The DSS displays these annotations in the variant list overlay and variant details page.

ClinVar is a public database of variant and phenotype relationships alongside supporting evidence and clinical interpretation histories.

  • Cellbase annotates whether a variant is present in Clinvar.
  • The DSS displays the ClinVar ID, interpretation, review status and number of entries alongside a link to the ClinVar record in the variant list and variant details page for germline variants.
  • The database version of ClinVar used by Cellbase is displayed in the DSS and may not always be the most recent. Please see the latest version of the Cancer Genome Analysis guide and Cellbase for further details.

The NGTD for cancer specifies which genomic tests are commissioned by the NHS in England, the technology by which they are available, and the patients who will be eligible to access to a test.

The DSS displays NGTD annotations in the tooltips of the genes shown in the variant grid and the gene information section of the variant details page.

NGTD annotations in the DSS depend on clinical indication groups. If the affected gene for a variant is present in the NGTD and is a target for any clinical indication within the same group as the patient's clinical indication (regardless of variant type), then the variant is annotated with the clinical indication group (e.g., Solid tumours) followed by all the clinical indication codes where the affected gene is a target (e.g., M1). If the affected gene is present in the NGTD but is a target for a different clinical indication group, the variant is simply annotated as present in the NGTD.

Info

The publication date of the NGTD file used is missing in the variant lists and detail pages of all cases ingested into the DSS between the 6.11.0 release (23/07/2025) and the 6.14.0 release (03/12/2025), please refer to the Cancer Genome Analysis guide for further details. The issue has been fixed as of the 6.14.0 release (03/12/2025) and any cases arriving to the DSS from this point onwards will be unaffected.

The GeL PanelApp knowledgebase allows virtual gene panels related to human disorders to be created, stored and queried and is used as the platform for achieving consensus on gene panels in the NHS Genomic Medicine Service (GMS).

  • The Ensembl gene ID of each variant is used to match the variant to Panels in PanelApp.
  • The Panels in which the affected gene is present are then shown on the variant list and variant details page.

Population germline allele frequency for the breakpoints of a given structural variant based on a panel of normals, which consists of germline structural variants observed in an internal Genomics England dataset of about 6,000 samples from unrelated individuals. If a variant has two breakpoints, maximal value of allele frequency among the two is reported. Not found suggests that this variant was not seen in the Genomics England dataset. If an SV is found to overlap with any SVs identified in the internal panels of normals, the population frequency will be annotated to the variant and displayed on the variant list and variant details page.

The Cancer Gene Census comprises a catalogue of genes which contain variants that have been causally implicated in cancer. In the Cancer DSS, we use the CGC database to annotate whether a gene is an oncogene, a tumour suppressor gene or both i.e., the role of the gene is ambiguous. For further information see Nature Reviews.

  • The affected gene of each variant is compared against the CGC data.
  • If a match is found, the annotation is attached to the affected gene and displayed in the DSS.