Variant Details Somatic SV¶

To open the variant details page, click 'View details' button on your chosen variant in the variant list.

On this page you can:

Variant and quality informationInterpretationGene informationPopulation FrequenciesQC FlagsResources

Variant and Quality Information¶

This panel allows you too view variant coordinates and quality metrics. You can also link out to view the variant in IGV

Key

#	Section	Description
1	GRCh38 coordinates	The chromosome and position for each breakpoint of the variant.
2	Chromosomal bands	The chromosomal band(s) overlapping this variant.
3	Reading frame	For variants that result in a gene fusion, this field will show the reading frame of the fusion product.
4	Paired reads	Paired reads support for structural variant called by Manta or JuLI (alt/total).
5	Split reads	Split reads support for structural variant called by Manta or JuLI (alt/total).
6	Variant type	The type of structural variant (e.g. inversion, duplication etc.)
7	VCF Filter	Shows whether the variant has passed the variant caller filters. For variants that haven’t passed, the reason is shown in red e.g. ‘LowDepth’ Tumor or normal sample read depth at this locus is below 2.
8	QC Flags	Flags that indicate a variant call may be of a lower quality and at greater risk of being a false positive. Hover over the QC flag for a description. See QC flags tab for more information.
9	Variant size	Variant size in KB
10	View in IGV	Click this to open the variant in IGV

This panel allows you to flag, classify, comment and export variants. Please refer to the Recording Interpretation documentation for more details.

This panel allows you to view information about the highest domained that overlaps this variant.

It includes:

Mode of action as listed in Cancer Gene Census (e.g. Oncogene, Tumor suppressor).
Domain as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide).
Matching clinical indications from the NHS National Genomic Test Directory (that also match the Clinical Indication Group of the patient).

Transcripts

By default, the canonical transcript is shown. But additional transcripts can be viewed by clicking 'Show alternative transcripts'

Key

#	Section	Description
1	Affected gene	HGNC Gene symbol.
2	Mode of action	Mode of action as defined in Cancer Gene Census (Oncogene, Tumor Suppressor gene, Ambiguous)
3	Domain	Domain as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide)
4	Presence in gene lists	Indicates if gene is listed in NHS National Genomic Test Directory (NGTD) and/or Cancer Gene Census. For NGTD, will also list Clinical Indications that match the patient's clinical indication group.
5	Ensembl Canonical Transcript ID	Ensembl Transcript ID for canonical transcript.
6	Impacted transcript region	Not yet implemented for SVs.
7	Alternative transcripts	Expandable table showing alternative (non-canonical) transcripts

Population germline allele frequency for the breakpoints of a given structural variant based on two internal panels of normals:

GESG germline variants from single germline analysis of ~ 2,200 samples.
GECG variants detected as germline in paired tumour-normal variant calling for ~ 2,500 cancer samples.

Description of the possible QC flags for somatic structural variants:

QC Flag	Description
H	Indel intersecting with reference homopolymers of at least 8 nucleotides in length
N	Indel in the regions with high levels of sequencing noise where at least 10% of the basecalls in a window extending 50 bases to either side of the indel's call have been filtered out due to the poor quality
PON	NOTE this is only calculated for VCF PASS variants. An SNV with a Phred score of Fisher's test of somatic allele ratio vs Panel of Normals (PoN) allele ratio < 50 (indicates systematic mapping/sequencing error).
GG	Variant with a germline allele frequency > 1% in gnomAD (indicates potential un-subtracted germline variant)
GE	Variant with a germline allele frequency > 1% in an internal Genomics England data set (indicates potential un-subtracted germline variant)
R	Recurrently identified somatic variant with somatic allele frequency > 5% in an internal Genomics England data set (indicates potential technical artefact)
SR	Variant overlapping simple repeats

This section includes link outs to resources which may be useful for somatic structural variant interpretation.

Info

Due to the nature of the resource and/or licensing constraints, we are only able to link out to the default home page for the above resources.

Last update: 2023-12-06