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BRIP1
Final classification
VUS
BRIP1 c.254C>T · p.Ser85Leu
BRIP1

NM_032043.3:c.254C>T (p.Ser85Leu) is a missense variant in BRIP1. PVS1 does not apply as this is not a null variant.

Gene
BRIP1
Transcript
NM_032043.3
HGVS · transcript:coding
NM_032043.3:c.254C>T
Consequence
N/A
GRCh38
chr17:61857183 G>A
GRCh37
chr17:59934544 G>A
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 benign; 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 benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
BRIP1 c.254C>T

NM_032043.3:c.254C>T (p.Ser85Leu) is a missense variant in BRIP1. PVS1 does not apply as this is not a null variant.1 This variant is present at extremely low frequency in population databases: gnomAD v2.1 at 0.00119% (3/251,440 alleles) and gnomAD v4.1 at 0.00099% (16/1,613,990 alleles), with no homozygotes observed. This meets the PM2 criterion at supporting strength for a rare variant in a gene associated with dominant cancer predisposition.2 Multiple in silico prediction tools support a benign effect: REVEL score 0.078 (strongly benign-leaning), BayesDel score -0.316 (benign), and SpliceAI max delta 0.03 (no predicted splicing impact). These concordant predictions meet BP4 at supporting benign strength.3 No functional studies have directly tested p.Ser85Leu. The largest BRIP1 missense functional characterization study (PMID:31822495) tested 20 helicase domain variants but did not include this residue. OncoKB reports no variant-specific functional evidence.4 ClinVar classifies this variant as Uncertain Significance (Variation ID: 141545) with 1-star review status based on 14 clinical laboratory submissions. No expert panel classification is available. This does not meet criteria for PP5 or BP6 application.5 No case-control studies, cosegregation data, de novo reports, or same-residue pathogenic comparators are available. BRIP1 missense variants in the helicase domain are a known disease mechanism (PMID:31822495), so BP1 does not apply despite this being a missense change.6 The combined evidence (PM2 supporting + BP4 supporting benign) yields conflicting benign and pathogenic signals. The overall classification is Variant of Uncertain Significance (VUS), consistent with the ClinVar consensus.7

PM2 + BP4 VUS
1 pvs1_variant_assessment
3 revelbayesdelspliceai ↗
7 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 · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_032043.3:c.254C>T is present at extremely low frequency in population databases: gnomAD v2.1 AF=1.19e-5 (3/251,440 alleles), gnomAD v4.1 AF=9.91e-6 (16/1,613,990 alleles), gnomAD-Canada absent. Both frequencies are well below the 0.1% PM2 threshold for a rare variant in a gene associated with dominant disease.
gnomAD v2.1: 3/251440 alleles (0.00119%)gnomAD v4.1: 16/1
BP4 supporting Benign
Multiple lines of computational evidence suggest NM_032043.3:c.254C>T does not impact gene product function. REVEL score is 0.078 (strongly benign-leaning, threshold for pathogenic is >0.5). BayesDel score is -0.316 (negative, indicating benign). SpliceAI max delta is 0.03 (no predicted splicing impact). These concordant predictions from independent algorithms support a benign interpretation.
REVEL: 0.078 (benign)BayesDel: -0.316 (benign)SpliceAI max delta: 0.03 (no splicing impact). Three independent algorithms concur on benign.
Assessed · not applied
Pathogenic
PS1 No different amino acid change at codon 85 has been established as pathogenic.
PS2 No de novo occurrence of NM_032043.3:c.254C>T has been reported in any reviewed publication or ClinVar submission.
PS3 No functional studies have directly tested NM_032043.3:c.254C>T (p.Ser85Leu).
PS4 No case-control studies demonstrate statistically significant enrichment of NM_032043.3:c.254C>T in affected individuals.
PM1 While p.Ser85Leu lies within the BRIP1 helicase domain (aa 1-888), a well-established functional domain, cancerhotspots.org does not identify this residue as a statistically significant mutational hotspot.
PM5 No different missense change at codon 85 has been classified as pathogenic in ClinVar.
PM6 No de novo occurrence of NM_032043.3:c.254C>T has been reported, with or without confirmed parentage.
PP1 No cosegregation data are available for NM_032043.3:c.254C>T.
PP2 PP2 requires a gene with a low rate of benign missense variation where missense variants are a common disease mechanism.
PP3 Multiple in silico prediction tools support a benign effect for NM_032043.3:c.254C>T.
PP4 No specific patient phenotype or family history data are available to evaluate.
PP5 ClinVar classifies NM_032043.3:c.254C>T as Uncertain Significance (Variation ID: 141545) with review status 'criteria provided, single submitter' (1 star).
Benign
BA1 gnomAD allele frequency is 0.00119% (v2.1) and 0.00099% (v4.1), well below the 1% BA1 threshold.
BS1 gnomAD allele frequency is 0.00119% (v2.1) and 0.00099% (v4.1), below the 0.3% BS1 threshold.
BS2 BS2 requires observation in a healthy adult individual for a disorder with full penetrance expected at an early age.
BS3 No functional studies demonstrate that NM_032043.3:c.254C>T (p.Ser85Leu) does not impair protein function.
BP1 BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease.
BP2 No evidence that NM_032043.3:c.254C>T has been observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant.
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease.
BP6 ClinVar classifies NM_032043.3:c.254C>T as Uncertain Significance (Variation ID: 141545, 1-star review).
N/A · 4 PVS1 · BS4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 9.91332e-06; MAF= 0.00099%, 16/1613990 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.20072e-05; MAF= 0.00320%, 2/62486 alleles, homozygotes = 0); grpmax FAF= 6.88e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.19313e-05; MAF= 0.00119%, 3/251440 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.63773e-05; MAF= 0.00264%, 3/113734 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00099% · 16 / 1,613,990
0 hom · FAF 0.00069%
Remaining individuals
2 / 62,486
0.0032%
European (non-Finnish)
14 / 1,179,970
0.0012%
+ 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0012% · 3 / 251,440
0 hom · FAF 0.0007%
European (non-Finnish)
3 / 113,734
0.0026%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
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 (13 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 141545)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.078. BayesDel score = -0.316079.
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 previously been reported in somatic cancers (COSMIC; COSV113270205, n = 1 times).
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 · 10 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
26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
26901136 ↗ Identification of Novel Candidate Genes for Early-Onset Colorectal Cancer Susceptibility. CLINVAR
31822495 ↗ Rare BRIP1 Missense Alleles Confer Risk for Ovarian and Breast Cancer. CLINVAR
20301575 ↗ Fanconi Anemia. CLINVAR
26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
26921362 ↗ No evidence that protein truncating variants in BRIP1 are associated with breast cancer risk: implications for gene panel testing. CLINVAR
29450531 ↗ Screening for Ovarian Cancer: US Preventive Services Task Force Recommendation Statement. CLINVAR
22964825 ↗ Screening for ovarian cancer: U.S. Preventive Services Task Force reaffirmation recommendation statement. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR