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BRIP1
Final classification
VUS
BRIP1 c.143C>A · p.Thr48Lys
BRIP1

NM_032043.3:c.143C>A (p.Thr48Lys) is a missense variant in BRIP1, a moderate-penetrance breast and ovarian cancer predisposition gene where the predominant disease mechanism is protein truncation.

Gene
BRIP1
Transcript
NM_032043.3
HGVS · transcript:coding
NM_032043.3:c.143C>A
Consequence
N/A
GRCh38
chr17:61859858 G>T
GRCh37
chr17:59937219 G>T
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, PP3 supporting, BP1 supporting benign; combination = 2 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, PP3 supporting, BP1 supporting benign; combination = 2 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2PP3 BP1 VUS
BRIP1 c.143C>A

NM_032043.3:c.143C>A (p.Thr48Lys) is a missense variant in BRIP1, a moderate-penetrance breast and ovarian cancer predisposition gene where the predominant disease mechanism is protein truncation.1 This variant is extremely rare in population databases: gnomAD v2.1 allele frequency is 0.00319% (1/31,388 alleles) and v4.1 allele frequency is 0.00037% (6/1,613,830 alleles) with no homozygotes observed, meeting PM2 at supporting strength.2 In silico analysis supports a deleterious effect: REVEL score of 0.728 exceeds the 0.7 threshold for damaging prediction; the Thr48Lys substitution is non-conservative, replacing a polar uncharged residue with a positively charged one, meeting PP3 at supporting strength.3 BRIP1 disease-causing mutations predominantly result in protein truncation or nonsense-mediated RNA decay. This missense variant is not consistent with the primary disease mechanism, meeting BP1 at supporting benign strength.4 This variant has been reported in ClinVar as Uncertain significance by 5 clinical laboratories (Variation ID 234642, 1-star review status). No functional studies, segregation data, de novo observations, or case-control data are available.5 No functional studies or literature directly testing NM_032043.3:c.143C>A (p.Thr48Lys) or a systematically characterized residue range including position 48 were identified. The variant has not been reported in COSMIC and OncoKB reports Unknown Oncogenic Effect.6 The evidence profile includes one pathogenic supporting criterion (PM2), one pathogenic supporting criterion (PP3), and one benign supporting criterion (BP1), resulting in net neutral evidence. Based on generic ACMG/AMP 2015 combination rules, this variant is classified as a Variant of Uncertain Significance.7

PM2 + PP3 + BP1 VUS
Gene diagram · NM_032043.3 · variants mapped to exon structure
BRIP1 NM_032043.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 21 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_032043.3:c.143C>A is extremely rare in population databases: gnomAD v2.1 allele frequency is 0.00319% (1/31,388 alleles, genomes only, 0 homozygotes) and gnomAD v4.1 allele frequency is 0.00037% (6/1,613,830 alleles, 0 homozygotes) with grpmax filtering allele frequency of 1.24×10⁻⁶. Both are well below the 0.1% threshold for PM2 at supporting strength.
gnomAD v2.1 AF = 0.00319% (1/31388 alleles)gnomAD v4.1 AF = 0.00037% (6/1
PP3 supporting Pathogenic
In silico analysis supports a deleterious effect of NM_032043.3:c.143C>A (p.Thr48Lys). REVEL score is 0.728, above the 0.7 threshold for damaging prediction. Multiple clinical laboratories (GeneDx, Ambry Genetics, LabCorp) also cite in silico evidence for a deleterious effect in their ClinVar submissions. BayesDel score is 0.307, which is borderline; however, the weight of evidence from REVEL and the non-conservative nature of the Thr→Lys substitution supports a deleterious prediction at the supporting level.
REVEL score = 0.728 (>0.7 damaging threshold)BayesDel score = 0.306828 (borderline)Thr→Lys is a non-conservative amino acid substitution (polar uncharged→positively charged)
BP1 supporting Benign
BRIP1 is a moderate-penetrance breast and ovarian cancer predisposition gene in which the predominant disease-causing mechanism is protein truncation. As established by Stratton and Rahman (2008, PMID:18163131), most disease-causing mutations in BRIP1 result in premature protein truncation or nonsense-mediated RNA decay, with only a small proportion likely to be rare missense variants disrupting critical functions. NM_032043.3:c.143C>A is a missense variant (p.Thr48Lys), and therefore BP1 applies at supporting benign strength.
Stratton & Rahman (2008): 'most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay' in BRIP1Missense variants are not the primary disease mechanism in BRIP1Position 48 (p.Thr48Lys) is in the N-terminal region outside the helicase domain
Assessed · not applied
Pathogenic
PVS1 NM_032043.3:c.143C>A is a missense variant (p.Thr48Lys) in BRIP1 exon 3.
PS1 No evidence of a different nucleotide change at codon 48 (same amino acid change p.Thr48Lys) that has been reported as pathogenic in the literature or databases.
PS2 No de novo occurrence data (with confirmed maternity and paternity) available for NM_032043.3:c.143C>A.
PS3 No functional studies were identified that directly tested NM_032043.3:c.143C>A (p.Thr48Lys) or a systematically characterized residue range that includes position 48.
PS4 No case-control studies or cohort data establishing statistically significant enrichment of NM_032043.3:c.143C>A in affected individuals versus controls are available.
PM1 Position 48 is located in the N-terminal region of BRIP1, outside the helicase domain (approximately residues 250–600).
PM5 No same-residue pathogenic comparator variant was identified at codon 48.
PM6 No de novo occurrence of NM_032043.3:c.143C>A has been reported.
PP1 No family segregation data are available for NM_032043.3:c.143C>A.
PP2 Insufficient data to assess whether BRIP1 has a low rate of benign missense variation.
PP4 No patient phenotype data or family history information is available for the individual(s) carrying NM_032043.3:c.143C>A.
PP5 No reputable source reports NM_032043.3:c.143C>A as pathogenic.
Benign
BA1 NM_032043.3:c.143C>A allele frequency is 0.00319% in gnomAD v2.1 and 0.00037% in gnomAD v4.1, both far below the 1% BA1 threshold.
BS1 NM_032043.3:c.143C>A allele frequency is 0.00319% in gnomAD v2.1 and 0.00037% in gnomAD v4.1, both far below the 0.3% BS1 threshold.
BS2 NM_032043.3:c.143C>A has not been observed in the homozygous state in gnomAD (0 homozygotes across v2.1 and v4.1 combined) and has not been reported in trans with a known pathogenic BRIP1 variant.
BS3 No well-established functional studies demonstrate that NM_032043.3:c.143C>A (p.Thr48Lys) has no deleterious effect on protein function or splicing.
BS4 No nonsegregation data are available for NM_032043.3:c.143C>A.
BP2 NM_032043.3:c.143C>A has not been observed in trans with a known pathogenic BRIP1 variant.
BP4 In silico analysis does not support a benign impact.
BP5 No alternate molecular basis for disease has been identified in an individual carrying NM_032043.3:c.143C>A.
BP6 No reputable source reports NM_032043.3:c.143C>A as benign.
N/A · 4 PM3 · PM4 · 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= 3.71786e-06; MAF= 0.00037%, 6/1613830 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 1.56226e-05; MAF= 0.00156%, 1/64010 alleles, homozygotes = 0); grpmax FAF= 1.24e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.18593e-05; MAF= 0.00319%, 1/31388 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.48593e-05; MAF= 0.00649%, 1/15418 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00037% · 6 / 1,613,830
0 hom · FAF 0.00012%
European (Finnish)
1 / 64,010
0.0016%
European (non-Finnish)
5 / 1,179,898
0.00042%
+ 8 not observed (Remaining individuals, Admixed American, Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0032% · 1 / 31,388
0 hom
European (non-Finnish)
1 / 15,418
0.0065%
+ 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 (5 clinical laboratories). (ClinVarID = 234642)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.728. BayesDel score = 0.306828.
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.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
The emerging landscape of breast cancer susceptibility.
Searched
c.143C>Ap.Thr48LysT48K143C
Found
Review by Stratton and Rahman describing the genetic architecture of breast cancer susceptibility, including BRIP1 as a rare moderate-penetrance gene. States that in BRIP1, 'most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay.' NM_032043.3:c.143C>A is not discussed.
Variant
◇ Residue / gene-level — variant not named
Applied to
BP1 supports · met
Why
Gene-level disease mechanism described; supports BP1 at supporting benign. Variant itself not mentioned.
In CHEK2, ATM, BRIP1 and PALB2, most of the disease-causing mutations result in premature protein truncation or nonsense-mediated RNA decay through nonsense codons or translational frameshifts.
Location Page 18, column 2, paragraph 1  ·  full text
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 6 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
31265121 ↗ Whole-exome sequencing of ovarian cancer families uncovers putative predisposition genes. CLINVAR
24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. CLINVAR
24366402 ↗ Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force. CLINVAR
31429903 ↗ Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: US Preventive Services Task Force Recommendation Statement. CLINVAR
35802134 ↗ ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). CLINVAR