chr13-32379893-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP5
The NM_000059.4(BRCA2):c.9097A>T(p.Thr3033Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T3033I) has been classified as Uncertain significance.
Frequency
Consequence
NM_000059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRCA2 | NM_000059.4 | c.9097A>T | p.Thr3033Ser | missense_variant | 23/27 | ENST00000380152.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRCA2 | ENST00000380152.8 | c.9097A>T | p.Thr3033Ser | missense_variant | 23/27 | 5 | NM_000059.4 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Molecular Section, Niloo Genom lab | - | The deceted heterozygous missense variant (T3033S) in exon 23 of the BRCA2 gene has not been previously published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. However, algorithms developed to predict changes on protein function (Mutation taster, Sift, etc.) support the pathogenic effect of the variant on the gene product but it has not been confirmed by functional studies. This variant is absent in population databases, indicating it is not a common benign variant in these populations. Based on available evidence and ACMG standards and guidelines this variant has been classified as likely pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at