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BRIP1
Final classification
VUS
BRIP1 c.1372G>C · p.Glu458Gln
BRIP1

NM_032043.3:c.1372G>C (p.Glu458Gln) is a missense variant in exon 10 of BRIP1.

Gene
BRIP1
Transcript
NM_032043.3
HGVS · transcript:coding
NM_032043.3:c.1372G>C
Consequence
N/A
GRCh38
chr17:61793698 C>G
GRCh37
chr17:59871059 C>G
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
BRIP1 c.1372G>C

NM_032043.3:c.1372G>C (p.Glu458Gln) is a missense variant in exon 10 of BRIP1. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with PM2 (supporting).1 Multiple computational tools predict no deleterious effect: REVEL score 0.334, BayesDel score -0.138785, and SpliceAI max delta 0.01, supporting BP4 (supporting).2 No well-established functional studies have been performed for this variant; OncoKB reports unknown oncogenic effect (PS3 and BS3 not met).3 ClinVar classifies this variant as Uncertain significance based on 2 clinical laboratory submissions (PS4, PP5 not met).4 No segregation data, de novo observations, case-control studies, or variant-specific publications were identified for this variant. This variant does not qualify as a null variant per ClinGen SVI PVS1 recommendations; PVS1 is not applicable.5 The evidence yields PM2 (supporting) and BP4 (supporting), which effectively cancel each other. Based on the ACMG/AMP 2015 framework, this variant is classified as Uncertain significance.6

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
5 pvs1_generic_framework ↗pvs1_variant_assessment
6 generic_acmg_combination_rules
Gene diagram · NM_032043.3 · variants mapped to exon structure
BRIP1 NM_032043.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_032043.3:c.1372G>C is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, indicating it is not present in large population cohorts. Allele frequency is below the 0.1% threshold for PM2 application.
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes/genomes).Absent from gnomAD-Canada v1.0 (genomes).
BP4 supporting Benign
Multiple lines of computational evidence suggest no deleterious impact. REVEL score is 0.334, BayesDel score is -0.138785 (negative/benign-leaning), and SpliceAI max delta score is 0.01 (no splicing impact). No computational tool predicts a pathogenic effect.
REVEL: 0.334 (sub-pathogenic).BayesDel: -0.138785 (benign-leaning).SpliceAI max delta: 0.01 (no predicted splicing impact).
Assessed · not applied
Pathogenic
PS3 No well-established in vitro or in vivo functional studies have been performed for NM_032043.3:c.1372G>C (p.Glu458Gln).
PS4 Variant has been observed in ClinVar as Uncertain significance (2 clinical laboratories) but no case-control data or statistically significant enrichment in affected individuals is available.
PP2 While loss-of-function is a known disease mechanism in BRIP1, insufficient evidence exists that missense variants are a predominant mechanism of disease in this gene with a low rate of benign missense variation.
PP3 Multiple computational tools do not support a deleterious effect.
PP5 ClinVar classification is Uncertain significance (2 clinical laboratories, criteria provided, single submitter), not a pathogenic classification from a reputable source.
Benign
BA1 Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 Variant is absent from gnomAD.
BS2 No evidence of homozygous occurrence or co-occurrence with a pathogenic variant in trans in a recessive gene.
BS3 No well-established in vitro or in vivo functional studies have been performed demonstrating no deleterious effect of NM_032043.3:c.1372G>C (p.Glu458Gln).
BS4 No segregation data available to demonstrate lack of co-segregation with disease.
BP1 While loss-of-function is a known disease mechanism in BRIP1 (associated with Fanconi anemia and hereditary breast/ovarian cancer), pathogenic missense variants have been reported in this gene.
BP6 This variant is not reported as benign or likely benign by a reputable source.
N/A · 12 PVS1 · PS1 · PS2 · PM1 · PM5 · PM6 · PP1 · PP4 · BP2 · BP3 · BP5 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 630785)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.334. BayesDel score = -0.138785.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRIP1, a DEAH helicase, is altered by mutation and amplification in various cancers, including breast cancer and melanoma.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 2 PMIDs not cited in assessment
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. CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR