Variant Details Somatic SV

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

Variant and quality informationInterpretationGene informationPopulation FrequenciesQC FlagsResources

Variant and Quality Information

This panel allows you to view variant and quality information including:

• Variant coordinates and quality metrics.
• Link out to view the variant in IGV.
• Link outs to variant entries in external databases and resources.

Key

#	Section	Description
1	GRCh38 coordinates	The chromosome and position for each breakpoint of the variant. If the genomic coordinates of a structural variant is shown as "Not available", the variant has been called by Pelops which detects the presence of a rearrangement, but not the precise breakpoint coordinates. Consequently, the partner break-end location also cannot be precisely determined, so Pelops returns a 1-2 kb region instead.
2	View in IGV	Click this to open the variant in IGV.
3	View in Decipher	Clicking on the Decipher link out will open the Decipher gene track within the genomic region specified by the variant GRCh38 coordinates.
4	Chromosomal bands	The chromosomal band(s) overlapping this variant. If the chromosomal bands of a structural variant is shown as "Not available", the variant has been called by Pelops as described above, and a chromsomal band cannot be provided as the precise breakpoint coordinate is unavailable.
5	Reading frame	For variants that result in a gene fusion, this field will show the reading frame of the fusion product.
6	Paired reads	Paired reads support for structural variants called by Manta or JuLI (alt/total).
7	Split reads	Split reads support for structural variants called by Manta or JuLI (alt/total).
8	Variant type	The type of structural variant (e.g. inversion, duplication etc.).
9	VCF Filter	Shows whether the variant has passed the variant caller filters. For variants that haven’t passed, the reason is shown in red.
10	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.
11	Origin	Indication of the variant’s origin as specified by TINC e.g. Somatic or Uncertain. This value will only be shown for cases that have gone through the TINC workflow.
12	Variant size	Variant size in KB.
Not shown*	Supporting reads per billion	Supporting reads per billion support for structural variants called by Pelops, including DUX4 fusions.
Not shown*	Allele depth	Allele depth support for internal tandem duplications called by Pindel.

Interpretation

This panel allows you to add interpretations to a variant, including:

• Flag a variant e.g., for further investigation.
• Classify according to the relevant guidelines.
• Comments.
• Export variants.

Please refer to the Recording Interpretation documentation for more details.

Gene information

This panel allows you to view information about the domained genes overlapping this variant.

It includes:

• Mode of action as listed in Cancer Gene Census e.g. Oncogene, Tumor suppressor, Ambiguous or Unknown.
• 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).
• Link outs to gene entries in external databases and resources.

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 of the affected gene.
2	Mode of action	Mode of action as defined in Cancer Gene Census i.e., Oncogene, Tumor Suppressor gene, Ambiguous or Unknown.
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, we will also list Clinical Indications that match the patient's clinical indication group.
5	Resource Linkouts	Linkouts to view entries releated to the gene in other resources e.g., "My Cancer Genome" database.
6	Ensembl Canonical Transcript ID	Ensembl Transcript ID for canonical transcript.
7	Impacted transcript region	Not yet implemented for SVs.
8	Alternative transcripts	Expandable table showing alternative (non-canonical) transcripts

Resource Linkouts

Clicking on the "My Cancer Genome" database link out will perform a search for the gene in the "Biomarkers" section of the database.

Population Frequencies

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.

QC Flags

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

Resources

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.

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Last update: 2025-03-11