Starting
Initialising…
0%
BRIP1
Final classification
VUS
BRIP1 c.611C>G · p.Ser204Cys
BRIP1

NM_032043.3:c.611C>G (p.Ser204Cys) is a missense variant in BRIP1 that is absent from all large population databases including gnomAD v2.1, v4.1, and gnomAD-Canada.

Gene
BRIP1
Transcript
NM_032043.3
HGVS · transcript:coding
NM_032043.3:c.611C>G
Consequence
N/A
GRCh38
chr17:61847117 G>C
GRCh37
chr17:59924478 G>C
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 moderate, BP4 supporting benign; combination = 1 moderate + 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
BRIP1 c.611C>G

NM_032043.3:c.611C>G (p.Ser204Cys) is a missense variant in BRIP1 that is absent from all large population databases including gnomAD v2.1, v4.1, and gnomAD-Canada.1 Multiple in silico predictors (REVEL 0.24, BayesDel -0.212, SpliceAI max delta 0.00) indicate this variant is tolerated and does not affect splicing.2 No variant-specific functional studies, case-control data, co-segregation data, or de novo observations were identified for this variant in the peer-reviewed literature. Applying generic ACMG/AMP 2015 classification rules (PMID:25741868): one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4) are met, resulting in insufficient evidence for classification; the variant is a Variant of Uncertain Significance (VUS).3

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
3 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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.24. BayesDel score = -0.212169.
      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