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BRIP1
Final classification
Likely Benign
BRIP1 c.476A>C · p.Lys159Thr
BRIP1

PM2 (supporting): The NM_032043.3:c.476A>C (p.Lys159Thr) missense variant in BRIP1 is absent from all large population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting level in the generic ACMG/AMP 2015 framework.

Gene
BRIP1
Transcript
NM_032043.3
HGVS · transcript:coding
NM_032043.3:c.476A>C
Consequence
N/A
GRCh38
chr17:61849160 T>G
GRCh37
chr17:59926521 T>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, BP1 supporting benign, BP4 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
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, BP1 supporting benign, BP4 supporting benign; combination = 1 supporting + 2 supporting benign, which maps to Likely Benign.
Classification rationale
PM2 BP1BP4 Likely Benign
BRIP1 c.476A>C

PM2 (supporting): The NM_032043.3:c.476A>C (p.Lys159Thr) missense variant in BRIP1 is absent from all large population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting level in the generic ACMG/AMP 2015 framework.1 BP1 (supporting benign): BRIP1 is a gene for which loss of function is the established disease mechanism. Truncating variants represent the primary pathogenic spectrum. This missense variant is not a predicted null variant, applying BP1 at supporting benign level.2 BP4 (supporting benign): Multiple computational predictors (REVEL 0.311, BayesDel 0.027, SpliceAI max delta 0.05) converge on a benign prediction with no evidence of splicing disruption, meeting BP4 at supporting benign level.3 The variant has one supporting pathogenic criterion (PM2) and two supporting benign criteria (BP1, BP4). Per ACMG/AMP 2015 combination rules, criteria at the supporting level in opposing directions do not sum to a definitive classification, and the variant is classified as a variant of uncertain significance (VUS).4

PM2 + BP1 + BP4 Likely Benign
2 pvs1_gene_contextpvs1_generic_framework ↗
3 revelbayesdelspliceai ↗
4 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 · 3 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 · supports benign
      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 = 0.05). REVEL score = 0.311. BayesDel score = 0.0269509.
      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