rs542551
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000059.4(BRCA2):c.9256+5252A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 216,724 control chromosomes in the GnomAD database, including 6,426 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).
Frequency
Consequence
NM_000059.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRCA2 | ENST00000380152.8 | c.9256+5252A>G | intron_variant | Intron 24 of 26 | 5 | NM_000059.4 | ENSP00000369497.3 | |||
BRCA2 | ENST00000530893.7 | c.8887+5252A>G | intron_variant | Intron 24 of 26 | 1 | ENSP00000499438.2 | ||||
BRCA2 | ENST00000614259.2 | n.*1314+5252A>G | intron_variant | Intron 23 of 25 | 2 | ENSP00000506251.1 |
Frequencies
GnomAD3 genomes AF: 0.224 AC: 33979AN: 151994Hom.: 4264 Cov.: 32
GnomAD4 exome AF: 0.258 AC: 16649AN: 64614Hom.: 2160 Cov.: 0 AF XY: 0.260 AC XY: 9870AN XY: 37904
GnomAD4 genome AF: 0.223 AC: 33994AN: 152110Hom.: 4266 Cov.: 32 AF XY: 0.222 AC XY: 16535AN XY: 74366
ClinVar
Submissions by phenotype
Breast-ovarian cancer, familial, susceptibility to, 2 Benign:1
Class 1 not pathogenic based on frequency >1% in an outbred sampleset. Frequency 0.1923 (Asian), 0.09959 (African), 0.248 (European), derived from 1000 genomes (2012-04-30). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at