rs774186567
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM4
The NM_000059.4(BRCA2):c.3634_3639del(p.Asn1212_Glu1213del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,568 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. D1210D) has been classified as Likely benign.
Frequency
Consequence
NM_000059.4 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRCA2 | NM_000059.4 | c.3634_3639del | p.Asn1212_Glu1213del | inframe_deletion | 11/27 | ENST00000380152.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRCA2 | ENST00000380152.8 | c.3634_3639del | p.Asn1212_Glu1213del | inframe_deletion | 11/27 | 5 | NM_000059.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250824Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135656
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461276Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 726836
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74474
ClinVar
Submissions by phenotype
Familial cancer of breast Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Aug 30, 2023 | - - |
Hereditary breast ovarian cancer syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2022 | ClinVar contains an entry for this variant (Variation ID: 462301). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. This variant is present in population databases (rs774186567, gnomAD 0.007%). This variant, c.3634_3639del, results in the deletion of 2 amino acid(s) of the BRCA2 protein (p.Asn1212_Glu1213del), but otherwise preserves the integrity of the reading frame. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at