0%
complete
Final classification
VUS
BRCA2
c.10111A>G
p.Thr3371Ala
missense · exon 27

BRCA2 encodes a DNA repair protein that maintains genome stability by repairing double-strand breaks through homologous recombination and by protecting DNA replication forks. It acts as a tumor suppressor, and inherited loss-of-function changes cause hereditary breast and ovarian cancer syndrome, with elevated lifetime risks of breast, ovarian, prostate, and pancreatic cancers; biallelic changes cause Fanconi anemia complementation group D1. Reduced or altered BRCA2 activity is implicated in multiple tumor types, and PARP inhibitors are an approved treatment for BRCA2-associated ovarian and breast cancers.

This variant

BRCA2 loss-of-function variants cause hereditary breast and ovarian cancer syndrome, yet this variant is a missense change (p.Thr3371Ala) of uncertain significance: available evidence neither establishes nor rules out pathogenicity. Clinically, it means the variant cannot yet be used to confirm or exclude BRCA2-related cancer risk, and its classification may change as more evidence accumulates.

Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.10111A>G
GRCh38
chr13:32398624 A>G
GRCh37
chr13:32972761 A>G
VUS: under the ENIGMA BRCA1/2 v1.2 rules no criterion was met, and the zero point score falls in the -1 to 5 VUS band. Flagged for human review: most criteria could not be evaluated from the available evidence, so this classification may change.
Classification rationale
VUS
BRCA2 c.10111A>G missense · exon 27

No ENIGMA BRCA1/2 v1.2 criteria-combination rule was satisfied because no criterion was met, and the zero evidence point score falls in the -1 to 5 VUS band, yielding a final classification of Variant of Uncertain Significance.

Gene diagram · NM_000059.4 · variants mapped to exon structure
BRCA2 NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 0 applied · 26 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 0

No criteria were applied for this variant.

Assessed · not applied · 0 not met · 26 not assessed
Pathogenic
PVS1 Not assessed: insufficient evidence was available to evaluate this criterion.
PS1 Not assessed: insufficient evidence was available to evaluate this criterion.
PS3 Not assessed: insufficient evidence was available to evaluate this criterion.
PS4 Not assessed: insufficient evidence was available to evaluate this criterion.
PM1 Not assessed: insufficient evidence was available to evaluate this criterion.
PM2 Not assessed: insufficient evidence was available to evaluate this criterion.
PM3 Not assessed: insufficient evidence was available to evaluate this criterion.
PM4 Not assessed: insufficient evidence was available to evaluate this criterion.
PM5 Not assessed: insufficient evidence was available to evaluate this criterion.
PP1 Not assessed: no co-segregation data were available; the ENIGMA multifactorial dataset records no segregation likelihood ratio for this variant.
PP2 Not assessed: insufficient evidence was available to evaluate this criterion.
PP3 Not assessed: insufficient evidence was available to evaluate this criterion.
PP4 Not assessed: insufficient evidence was available to evaluate this criterion.
PP5 Not assessed: insufficient evidence was available to evaluate this criterion.
Benign
BA1 Not assessed: insufficient evidence was available to evaluate this criterion.
BS1 Not assessed: insufficient evidence was available to evaluate this criterion.
BS2 Not assessed: insufficient evidence was available to evaluate this criterion.
BS3 Not assessed: insufficient evidence was available to evaluate this criterion.
BS4 Not assessed: no non-segregation data were available; no segregation likelihood ratio or affected non-carriers are reported for this variant.
BP1 Not assessed: insufficient evidence was available to evaluate this criterion.
BP2 Not assessed: insufficient evidence was available to evaluate this criterion.
BP3 Not assessed: insufficient evidence was available to evaluate this criterion.
BP4 Not assessed: insufficient evidence was available to evaluate this criterion.
BP5 Not assessed: insufficient evidence was available to evaluate this criterion.
BP6 Not assessed: insufficient evidence was available to evaluate this criterion.
BP7 Not assessed: insufficient evidence was available to evaluate this criterion.
N/A · 2 PS2 · PM6
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= 1.05323e-05; MAF= 0.00105%, 17/1614084 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000200454; MAF= 0.02005%, 9/44898 alleles, homozygotes = 0); grpmax FAF= 0.00010391.
v2.1
This variant is present in gnomAD v2.1 (AF= 7.07504e-06; MAF= 0.00071%, 2/282684 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000100241; MAF= 0.01002%, 2/19952 alleles, homozygotes = 0).
🇨🇦 CA
This variant is present in gnomAD-Canada v1.0 (AF= 0.00043426338074041906, 8/18422 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0011% · 17 / 1,614,084
0 hom · FAF 0.01%
East Asian
9 / 44,898
0.02%
Remaining individuals
8 / 62,486
0.013%
+ 8 not observed (Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
gnomAD v2.1
0.00071% · 2 / 282,684
0 hom
East Asian
2 / 19,952
0.01%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
0.043% · 8 / 18,422
0 hom · FAF 0.2%
East Asian
6 / 1,338
0.45%
Remaining individuals
2 / 1,138
0.18%
+ 7 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, European (Finnish), Middle Eastern, European (non-Finnish), South Asian)
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely benign (9 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Benign (2 clinical laboratories). (ClinVarID = 37720)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.093. BayesDel score = -0.538317.
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. BRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
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; COSV116004818, n = 2 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 9 PMIDs not cited in assessment
20104584 ↗ Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. CLINVAR
24817641 ↗ An integrated in silico approach to analyze the involvement of single amino acid polymorphisms in FANCD1/BRCA2-PALB2 and FANCD1/BRCA2-RAD51 complex. CLINVAR
25682074 ↗ Prevalence of BRCA1 and BRCA2 germline mutations in patients with triple-negative breast cancer. CLINVAR
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
27376475 ↗ Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. CLINVAR
12692171 ↗ American Society of Clinical Oncology policy statement update: genetic testing for cancer susceptibility. CLINVAR
20301534 ↗ PAX6 Aniridia Syndrome. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR