chr17-61716037-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_032043.3(BRIP1):c.2406C>T(p.Asp802Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000872 in 1,604,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_032043.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249618Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135010
GnomAD4 exome AF: 0.00000757 AC: 11AN: 1452966Hom.: 0 Cov.: 30 AF XY: 0.00000415 AC XY: 3AN XY: 722414
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152024Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74230
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
- -
- -
The BRIP1 p.Asp802= variant was not identified in the literature nor was it identified in the ClinVar, Cosmic, MutDB, and Zhejiang Colon Cancer Database. The variant was identified in dbSNP (ID: rs748981650), and in control databases in 10 of 275524 chromosomes at a frequency of 0.00004 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: “Other” in 1 of 6428 chromosomes (freq: 0.0002), and East Asian in 9 of 18502 chromosomes (freq: 0.0005); but not in the African, Latino, European Non-Finnish, Ashkenazi Jewish, European Finnish, and South Asian populations. The p.Asp802= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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 uncertain significance. -
Hereditary cancer-predisposing syndrome Benign:2
- -
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Familial cancer of breast;C1836860:Fanconi anemia complementation group J Benign:1
- -
Familial cancer of breast Benign:1
This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at