About BRCA2
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
BRCA2 c.8009C>G, p.(Ser2670Trp)
Classification
Uncertain significance
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is ClinGen BRCA2 VCEP v1.2.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 2
Benign evidence criteria: 1
Pathogenic criteria applied · 2
PM2Supporting
PM2 · supporting
This variant is absent from gnomAD v2.1 and absent from gnomAD v4.1, which supports rarity in population controls under the BRCA2 VCEP framework. This meets PM2 at supporting strength.
PP5Supporting
PP5 · supporting
Expert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Pathogenic.
Benign criteria applied · 1
BP4Supporting
BP4 · supporting
This missense variant lies within the BRCA2 DNA-binding region used by the BRCA2 VCEP bioinformatic framework, and computational evidence supports no predicted impact under that rule. BayesDel no-AF is 0.159332, which is at or below the BP4 threshold of 0.18, and SpliceAI max delta score is 0.03, which is at or below the BP4 threshold of 0.1. These findings support BP4 at supporting strength.
Recorded classification: Uncertain significance
ENIGMA BRCA1/BRCA2 Specification v1.2 final-classification framework (Table 3 with ENIGMA conflicting-evidence point system)
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
SpliceAI score
0.030 maximum delta
Recorded SpliceAI maximum delta score: 0.030. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
5 reported laboratory submissions
3 Likely pathogenic · 1 Pathogenic · 1 Uncertain significance.
Functional evidence
Statement recorded
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2.0, with the data and sources behind each one.
28 criteria with recorded statuses: 3 met · 7 not met · 8 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
The BRCA2 c.8009C>G (p.Ser2670Trp) variant has not been observed in COSMIC and has been reported in ClinVar, including a Pathogenic expert-panel classification by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel.
This variant is absent from gnomAD v2.1 and absent from gnomAD v4.1, supporting rarity in population controls and meeting PM2_Supporting under the BRCA2 VCEP framework.
In the BRCA2 VCEP functional assay table, this variant is recorded with splice alteration evidence including exon 18 deletion, but the reviewed evidence was not accepted for PS3 or BS3 code application, so neither functional criterion is met from the available curated data.
For computational evidence, REVEL is 0.825, but the BRCA2 VCEP rule uses BayesDel and SpliceAI; BayesDel no-AF is 0.159332 and SpliceAI max delta score is 0.03, which supports BP4 and does not meet PP3 thresholds.
No criteria match.
Met · 3
PM2 SupportingThis variant is absent from gnomAD v2.1 and absent from gnomAD v4.1, which supports rarity in population controls under the BRCA2 VCEP framework. This meets PM2 at supporting strength. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PM2_Supporting: absent from gnomAD exome and genome datasets, with regional read-depth quality safeguards.
Evidence considered
- Absent from gnomAD v2.1.
- Absent from gnomAD v4.1.
Still missing
- Average read-depth confirmation at this locus was not separately provided in the reviewed files.
Sources
PP5 SupportingExpert panel ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen classified as Pathogenic. Details ▾Hide ▴
BP4 SupportingThis missense variant lies within the BRCA2 DNA-binding region used by the BRCA2 VCEP bioinformatic framework, and computational evidence supports no predicted impact under that rule. BayesDel no-AF is 0.159332, which is at or below the BP4 threshold of 0.18, and SpliceAI max delta score is 0.03, which is at or below the BP4 threshold of 0.1. These findings support BP4 at supporting strength. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BP4 applies to missense/in-frame variants inside a clinically important domain when BayesDel no-AF ≤0.18 and SpliceAI ≤0.1.
Evidence considered
- Protein position 2670 lies within the BRCA2 DNA-binding domain 2481-3186.
- BayesDel no-AF score 0.159332.
- SpliceAI max delta score 0.03.
Sources
Not met · 7 · evaluated, threshold not reached
PVS1 This is a missense substitution, NM_000059.3:c.8009C>G (p.Ser2670Trp), rather than a nonsense, frameshift, canonical ±1/2 splice-site, initiation-codon, or exon-level deletion/duplication variant. SpliceAI predicts no significant splice effect (max delta score 0.03), so available evidence does not support applying PVS1. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PVS1 applies to null variants or qualifying RNA-only loss-of-function evidence.
Evidence considered
- BRCA2 VCEP framework recognizes loss of function as a disease mechanism
- but this variant is not in a default PVS1 variant class.
- SpliceAI max delta score 0.03 does not support a strong splice-loss mechanism.
Still missing
- RNA data specifically qualifying this variant for PVS1(RNA) were not identified in the available reviewed sources.
Sources
PS3 In the BRCA2 VCEP functional table, this variant is recorded as a missense variant with splice alteration evidence, including exon 18 deletion, but the available evidence was not accepted for PS3 code application. The table states that results from one calibrated study with a cDNA-based design were not considered for code application, so PS3 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PS3 requires well-established functional studies supportive of a damaging effect, with code recommendations taken from calibrated published assays in Table 9.
Evidence considered
- VCEP Table 9 entry for BRCA2 c.8009C>G lists code 'None / N/A' and notes PS3 and BS3 not met.
Still missing
- Direct review of the underlying assay reports could further clarify the splice effects
- but the VCEP table does not support PS3 for this variant.
Sources
PP3 This missense variant lies within the BRCA2 DNA-binding region used by the BRCA2 VCEP bioinformatic framework, but the computational thresholds for PP3 are not met. BayesDel no-AF is 0.159332, which is below the pathogenic threshold of 0.30, and SpliceAI max delta score is 0.03, which is below the splice threshold of 0.2. REVEL is 0.825, but the BRCA2 VCEP rule uses BayesDel and SpliceAI rather than REVEL for PP3/BP4 adjudication. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PP3 applies to missense/in-frame variants in a clinically important domain with BayesDel no-AF ≥0.30, or to variants with SpliceAI ≥0.2.
Evidence considered
- BayesDel no-AF score 0.159332.
- SpliceAI max delta score 0.03.
- REVEL score 0.825.
Sources
BA1 This variant is absent from gnomAD v2.1 and absent from gnomAD v4.1, so its population frequency is well below the BA1 stand-alone benign threshold of filter allele frequency greater than 0.1%. BA1 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BA1 requires filter allele frequency >0.1% in qualifying gnomAD populations.
Evidence considered
- Absent from gnomAD v2.1.
- Absent from gnomAD v4.1.
Sources
BS1 This variant is absent from gnomAD v2.1 and absent from gnomAD v4.1, so its population frequency is below the BS1 thresholds of filter allele frequency above 0.002% or 0.01%. BS1 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BS1_Supporting requires FAF >0.002% and ≤0.01%; BS1 requires FAF >0.01% in qualifying populations.
Evidence considered
- Absent from gnomAD v2.1.
- Absent from gnomAD v4.1.
Sources
BS3 In the BRCA2 VCEP functional table, this variant is recorded as having splice alteration evidence, including exon 18 deletion, but the available evidence was not accepted for BS3 code application. The table states that PS3 and BS3 are not met for this variant. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BS3 requires well-established functional studies showing no damaging effect, with code recommendations taken from calibrated published assays in Table 9.
Evidence considered
- VCEP Table 9 entry for BRCA2 c.8009C>G lists code 'None / N/A' and notes PS3 and BS3 not met.
Still missing
- Direct review of the underlying assay reports could further clarify the splice effects
- but the VCEP table does not support BS3 for this variant.
Sources
BP1 This missense variant is located within the BRCA2 DNA-binding region (amino acids 2481-3186), which is treated as a clinically important functional domain in the BRCA2 VCEP framework. Because BP1_Strong requires a missense or silent variant outside a clinically important functional domain and with no predicted splice effect, BP1 is not met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BP1_Strong applies outside clinically important functional domains with SpliceAI ≤0.1.
Evidence considered
- Protein position 2670 falls within the BRCA2 DNA-binding domain 2481-3186.
- SpliceAI max delta score 0.03.
Sources
Not assessed · 8 · no assessment recorded
PS1 No previously established pathogenic or likely pathogenic variant causing the same amino acid change or the same predicted splicing outcome was identified in the reviewed materials, so PS1 was not assessed from the available evidence. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PS1 requires the same amino acid change as a previously established pathogenic/likely pathogenic variant acting through protein effect, or the same predicted splicing impact as a previously classified pathogenic/likely pathogenic variant.
Evidence considered
- PS1 requires a previously classified pathogenic or likely pathogenic comparator with the same amino acid change or same splicing effect under the BRCA2 VCEP rules.
Still missing
- A dedicated same-amino-acid and same-splice-effect comparator review was not available in the retrieved materials.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
PS4 No case-control study or other reviewed dataset was identified showing that this variant is significantly enriched in affected individuals with an odds ratio of at least 4 and p value of 0.05 or less. Available evidence is insufficient to assess PS4. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PS4 requires significant enrichment in affected individuals versus controls; if case-control LR estimates are available they are preferred under PP4/BP5 rather than PS4.
Evidence considered
- The reviewed VCEP-supporting resources did not provide qualifying PS4 evidence for this variant.
Still missing
- No ethnicity-matched case-control analysis for this variant was identified.
- No qualifying odds ratio or confidence interval was identified.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18vcep_supplementarytables_v1_2_2024_11_18vcep_humu_40_1557_s001
PM3 No evidence was identified that this variant was observed in trans with a pathogenic BRCA2 variant in a proband with phenotype consistent with BRCA2-related Fanconi anemia. PM3 was not assessed. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PM3 is used only for qualifying Fanconi-anemia cases with co-occurring variants in trans.
Evidence considered
- PM3 in this framework is restricted to BRCA2-related Fanconi-anemia settings.
Still missing
- No biallelic BRCA2 case data with Fanconi-anemia phenotype were identified.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
PP1 No quantitative co-segregation analysis or family likelihood ratio for this variant was identified in the reviewed materials, so PP1 was not assessed. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PP1 requires quantitative co-segregation analysis meeting LR thresholds.
Evidence considered
- PP1 in this framework requires quantitative segregation evidence.
Still missing
- No pedigree-based segregation likelihood ratio was identified.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
PP4 The BRCA2 clinical-history likelihood-ratio workbook did not identify an entry for this exact variant, so no variant-specific multifactorial clinical-history likelihood ratio was available to assess PP4. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PP4 uses calibrated multifactorial clinical-history likelihood ratios, with Supporting at LR ≥2.08, Moderate at LR ≥4.3, and Strong at LR ≥18.7.
Evidence considered
- No exact variant match was found in the BRCA2 clinical-history LR table.
Still missing
- No exact-match clinical-history LR entry was identified in the BRCA2 Li et al. workbook.
Sources
BS2 No qualifying observations in individuals without features of BRCA2-related Fanconi anemia were identified for this variant, so BS2 was not assessed. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BS2 uses a point-based framework in the absence of Fanconi-anemia features.
Evidence considered
- BS2 in this framework requires point-based evidence from individuals lacking Fanconi-anemia features.
Still missing
- No proband-level BS2 point data were identified.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
BS4 No quantitative non-segregation analysis or family likelihood ratio against pathogenicity was identified for this variant, so BS4 was not assessed. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BS4 requires quantitative lack-of-segregation evidence meeting benign LR thresholds.
Evidence considered
- BS4 in this framework requires quantitative segregation evidence.
Still missing
- No pedigree-based non-segregation likelihood ratio was identified.
Sources
BP5 The BRCA2 clinical-history likelihood-ratio workbook did not identify an entry for this exact variant, so no variant-specific multifactorial clinical-history likelihood ratio was available to assess BP5. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BP5 uses calibrated multifactorial clinical-history likelihood ratios, with Supporting at LR ≤0.48, Moderate at LR ≤0.23, and Strong at LR ≤0.05.
Evidence considered
- No exact variant match was found in the BRCA2 clinical-history LR table.
Still missing
- No exact-match clinical-history LR entry was identified in the BRCA2 Li et al. workbook.
Sources
Not applicable · 10· recorded as not applicable Show reasons ▾Hide reasons ▴
PS2 VCEPDe novo occurrence evidence is not used in this BRCA2 specification, so PS2 is not applicable. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2.
Evidence considered
- The BRCA2 VCEP specification marks PS2 as not applicable.
Sources
PM1 VCEPPM1 is not applied in this BRCA2 specification because domain and hotspot information are incorporated into the bioinformatic framework rather than used as a separate criterion. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2; domain information is captured under the bioinformatic framework.
Evidence considered
- The BRCA2 VCEP specification marks PM1 as not applicable.
Sources
cspec ↗vcep_specifications_v1_2_2024_11_18
PM4 VCEPPM4 is not used in this BRCA2 specification. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2.
Evidence considered
- The BRCA2 VCEP specification marks PM4 as not applicable.
Sources
PM5 N/AFor BRCA2, PM5 is repurposed for protein-truncating-variant logic rather than classic same-residue missense comparison. Because this is a missense variant and the PM5 candidate review marked classic same-residue PM5 as ineligible, PM5 is not applicable. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PM5 is used for PTC logic according to exon-specific Table 4 rules, not classic same-residue missense PM5, for this gene framework.
Evidence considered
- PM5 candidate artifact states that BRCA2 uses a PTC-specific PM5 mode and classic same-residue PM5 is not eligible for this variant.
Sources
PM6 VCEPAssumed de novo evidence is not used in this BRCA2 specification, so PM6 is not applicable. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2.
Evidence considered
- The BRCA2 VCEP specification marks PM6 as not applicable.
Sources
PP2 VCEPPP2 is not used in this BRCA2 specification. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2.
Evidence considered
- The BRCA2 VCEP specification marks PP2 as not applicable.
Sources
BP2 VCEPBP2 is not used in this BRCA2 specification except in the context of BS2, and no such BS2 context was identified here. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2 outside the BS2 context.
Evidence considered
- The BRCA2 VCEP specification marks BP2 as not applicable outside BS2 context.
Sources
BP3 VCEPBP3 is not used in this BRCA2 specification. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2.
Evidence considered
- The BRCA2 VCEP specification marks BP3 as not applicable.
Sources
BP6 VCEPBP6 is not used in this BRCA2 specification. Details ▾Hide ▴
VCEP rule
Not applicable in ENIGMA BRCA2 v1.2.
Evidence considered
- The BRCA2 VCEP specification marks BP6 as not applicable.
Sources
BP7 N/ABP7 in this BRCA2 specification is intended for silent or intronic variants, or for RNA-only evidence showing no damaging splice effect in qualifying settings. This is a missense variant, and the reviewed functional table did not support a benign RNA-based code for this variant, so BP7 is not applicable. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BP7 is limited to silent/intronic contexts or qualifying RNA-only benign evidence frameworks.
Evidence considered
- Variant type is missense.
- Table 9 does not assign a benign RNA-based code for this variant.
- SpliceAI max delta score is 0.03.
Sources
Identifiers
- Gene
- BRCA2
- Transcript
- NM_000059.3
- Coding (HGVS c.)
- NM_000059.3:c.8009C>G
- Protein (HGVS p.)
- NP_000050.2:p.(Ser2670Trp)
- GRCh38
- chr13:32363211 C>G
- GRCh37
- chr13:32937348 C>G
- ClinVar
- 489785
Gene diagram
Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.3. Select a row to find it on the plot.
BRCA2NM_000059.3
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in BRCA2
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.825
- BayesDel
- 0.159
How the predictions were used
BP4 SupportingThis missense variant lies within the BRCA2 DNA-binding region used by the BRCA2 VCEP bioinformatic framework, and computational evidence supports no predicted impact under that rule. BayesDel no-AF is 0.159332, which is at or below the BP4 threshold of 0.18, and SpliceAI max delta score is 0.03, which is at or below the BP4 threshold of 0.1. These findings support BP4 at supporting strength. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BP4 applies to missense/in-frame variants inside a clinically important domain when BayesDel no-AF ≤0.18 and SpliceAI ≤0.1.
Evidence considered
- Protein position 2670 lies within the BRCA2 DNA-binding domain 2481-3186.
- BayesDel no-AF score 0.159332.
- SpliceAI max delta score 0.03.
Sources
PP3 This missense variant lies within the BRCA2 DNA-binding region used by the BRCA2 VCEP bioinformatic framework, but the computational thresholds for PP3 are not met. BayesDel no-AF is 0.159332, which is below the pathogenic threshold of 0.30, and SpliceAI max delta score is 0.03, which is below the splice threshold of 0.2. REVEL is 0.825, but the BRCA2 VCEP rule uses BayesDel and SpliceAI rather than REVEL for PP3/BP4 adjudication. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 PP3 applies to missense/in-frame variants in a clinically important domain with BayesDel no-AF ≥0.30, or to variants with SpliceAI ≥0.2.
Evidence considered
- BayesDel no-AF score 0.159332.
- SpliceAI max delta score 0.03.
- REVEL score 0.825.
Sources
BP7 N/ABP7 in this BRCA2 specification is intended for silent or intronic variants, or for RNA-only evidence showing no damaging splice effect in qualifying settings. This is a missense variant, and the reviewed functional table did not support a benign RNA-based code for this variant, so BP7 is not applicable. Details ▾Hide ▴
Rule
ENIGMA BRCA2 v1.2 BP7 is limited to silent/intronic contexts or qualifying RNA-only benign evidence frameworks.
Evidence considered
- Variant type is missense.
- Table 9 does not assign a benign RNA-based code for this variant.
- SpliceAI max delta score is 0.03.
Sources
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.825. BayesDel score = 0.159332.
8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
-
PMID 29394989 ↗Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.No paper-specific finding is recorded.
-
PMID 16489001 ↗Genetic and histopathologic evaluation of BRCA1 and BRCA2 DNA sequence variants of unknown clinical significance.No paper-specific finding is recorded.
-
PMID 12228710 ↗BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.Yang H et al. · 2002No paper-specific finding is recorded.
-
PMID 23096355 ↗BRCA1 and BRCA2 mutations in breast cancer patients from Venezuela.Lara K et al. · 2012No paper-specific finding is recorded.
-
PMID 23108138 ↗A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity.Guidugli L et al. · 2013No paper-specific finding is recorded.
-
PMID 24013206 ↗A cancer-associated BRCA2 mutation reveals masked nuclear export signals controlling localization.No paper-specific finding is recorded.
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PMID 25741868 ↗Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.No paper-specific finding is recorded.
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PMID 28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.No paper-specific finding is recorded.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.030
Open source ↗
ClinVar
3 Likely pathogenic · 1 Pathogenic · 1 Uncertain significance
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
ClinGen CSpec
Captured ClinGen CSpec source record
Open source ↗
All source links
- ClinGen CSpec ↗cspec.genome.network/cspec/ui/svi/doc/1535438831
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/489785/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/13-32937348-C-G?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr13-32363211-C-G?dataset=gn…
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000059.3%3Ac.8009…
- OncoKB ↗www.oncokb.org/gene/BRCA2/S2670W
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=BRCA2+c.8009C%3EG
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
ClinVar
This variant has been reported in ClinVar as Likely pathogenic (3 clinical laboratories) and as Pathogenic (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory) and as Pathogenic by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 489785)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.825. BayesDel score = 0.159332.
Functional
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.