rs2305635
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015175.3(NBEAL2):c.4995G>A(p.Val1665Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 1,550,500 control chromosomes in the GnomAD database, including 119,430 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_015175.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.346 AC: 52658AN: 152012Hom.: 9565 Cov.: 34
GnomAD3 exomes AF: 0.364 AC: 55393AN: 152366Hom.: 10592 AF XY: 0.374 AC XY: 30402AN XY: 81324
GnomAD4 exome AF: 0.393 AC: 549865AN: 1398370Hom.: 109867 Cov.: 71 AF XY: 0.395 AC XY: 272732AN XY: 689836
GnomAD4 genome AF: 0.346 AC: 52654AN: 152130Hom.: 9563 Cov.: 34 AF XY: 0.348 AC XY: 25921AN XY: 74382
ClinVar
Submissions by phenotype
not specified Benign:3
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not provided Benign:2
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Gray platelet syndrome Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at