NM_000059.4:c.7051G>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_000059.4(BRCA2):c.7051G>A(p.Ala2351Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A2351G) has been classified as Likely benign.
Frequency
Consequence
NM_000059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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BRCA2 | ENST00000380152.8 | c.7051G>A | p.Ala2351Thr | missense_variant | Exon 14 of 27 | 5 | NM_000059.4 | ENSP00000369497.3 | ||
BRCA2 | ENST00000530893.7 | c.6682G>A | p.Ala2228Thr | missense_variant | Exon 14 of 27 | 1 | ENSP00000499438.2 | |||
BRCA2 | ENST00000614259.2 | n.7051G>A | non_coding_transcript_exon_variant | Exon 13 of 26 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250694Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135572
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1461174Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726886
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74386
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Uncertain:3
ACMG classification criteria: BP4 supporting -
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The BRCA2 c.7051G>A (p.Ala2351Thr) missense change has a maximum subpopulation frequency of 0.020% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, and to our knowledge functional studies have not been performed. This variant has been reported in individuals with breast and ovarian cancer (PMID: 18284688, 21965345) and a case-control study indicated that individuals with this variant had an increased risk of developing breast cancer with an odds ratio of 1.6 (PMID: 30287823). However, this variant has also been reported in individuals who harbored a pathogenic variant in BRCA1 or BRCA2 (UMD, NHGRI BIC databases). This variant is absent in the FLOSSIES database, which contains genetic variants from women older than 70 years of age who have never had cancer (https://whi.color.com/). To our knowledge, this variant has not been reported in individuals with Fanconi anemia. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance. -
not specified Uncertain:1Benign:1
Variant summary: BRCA2 c.7051G>A (p.Ala2351Thr) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 6.7e-05 in 298156 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in BRCA2 causing Hereditary Breast and Ovarian Cancer Syndrome (6.7e-05 vs 0.00075), allowing no conclusion about variant significance. c.7051G>A has been reported in the literature in individuals affected with breast or ovarian cancer (example: Akbari_2011, Lee_2008, Momozawa_2018, Park_2020) as well as in controls (Momozawa_2018). These reports however, do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer Syndrome. Co-occurrences with other pathogenic variants have been reported in UMD and NHGRI BIC databases (BRCA2 c.1723A>T, p.Lys575X; BRCA1 c.2411_2412delAG, p.Gln804Leufs), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Eight ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=7) or likely benign (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance. -
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Familial cancer of breast Uncertain:1Benign:1
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ACMG codes applied following ENIGMA VCEP rules: BP1_STR, BS1_SUP; BP5_MOD -
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
The p.A2351T variant (also known as c.7051G>A), located in coding exon 13 of the BRCA2 gene, results from a G to A substitution at nucleotide position 7051. The alanine at codon 2351 is replaced by threonine, an amino acid with similar properties. This alteration has been reported with a carrier frequency of 4 in 7,051 unselected breast cancer patients and 4 in 11,241 female controls of Japanese ancestry (Momozawa Y et al. Nat Commun. 2018 10;9:4083). This alteration has also been reported in 1 of 1345 ovarian cancer patients (Akbari MR et al. J. Med. Genet. 2011 Nov;48:783-6) and in a cohort of 1469 early-onset breast cancer patients (Lee E et al. Breast Cancer Res. 2008 Mar;10:R19). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
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Hereditary breast ovarian cancer syndrome Uncertain:1Benign:1
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Medulloblastoma;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Uncertain:1
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Medulloblastoma;C0040588:Tracheoesophageal fistula;C0346153:Familial cancer of breast;C0376358:Malignant tumor of prostate;C1838457:Fanconi anemia complementation group D1;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2;C2751641:Glioma susceptibility 3;C3150546:Pancreatic cancer, susceptibility to, 2;CN033288:Wilms tumor 1 Uncertain:1
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Malignant tumor of breast Uncertain:1
The BRCA2 p.Ala2351Thr variant was identified by Akbari (2011) in an individual with ovarian cancer. The variant was also identified in dbSNP (ID: rs80358930) “With unknown allele”, and in the BIC database (4X with unknown clinical importance). The variant was also identified the Exome Aggregation Consortium (ExAC) database (released Oct 20th, 2014) in 7 of 120970 chromosomes (frequency: 0.0000) (or 4 South Asian, 1 East Asian, 2 European (Non-Finnish) individuals) and none from a population of Other/African/Latino/European (Finnish) individuals; COSMIC, the ClinVar database (classified as a uncertain significance by BIC, classified as uncertain significance by Ambry Genetics, and classification not provided by Invitae) and UMD (3X as a 3-unclassified variant). In UMD the variant was identified with a co-occurring pathogenic BRCA2 variant (c.1723A>T, p.Lys575X), increasing the likelihood that the p.Ala2351Thr variant does not have clinical significance. In addition, Myriad classifies this variant as a polymorphism (personal communication).The BRCA2 IARC database notes that there is a weak/null probability of creating a de novo splice donor at nt #7046 and a weak/null probability to create a de novo splice acceptor at nt #7063. The p.Ala2351 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD) provide inconsistent predictions regarding the impact of the variant amino acid on the protein; this information is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of unknown significance. -
not provided Benign:1
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Observed in individuals with early onset breast cancer or ovarian cancer (Lee 2008, Akbari 2011); This variant is associated with the following publications: (PMID: 10923033, 31131967, 30287823, 28111427, 21965345, 18284688, 25348012, 25583476) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at