rs2287363
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015354.3(NUP188):c.4596A>C(p.Ser1532Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 1,612,342 control chromosomes in the GnomAD database, including 149,330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_015354.3 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: 0.438 AC: 66560AN: 151884Hom.: 14686 Cov.: 32
GnomAD3 exomes AF: 0.435 AC: 108657AN: 249614Hom.: 23996 AF XY: 0.430 AC XY: 58104AN XY: 135170
GnomAD4 exome AF: 0.428 AC: 624941AN: 1460342Hom.: 134613 Cov.: 61 AF XY: 0.426 AC XY: 309655AN XY: 726548
GnomAD4 genome AF: 0.438 AC: 66647AN: 152000Hom.: 14717 Cov.: 32 AF XY: 0.440 AC XY: 32684AN XY: 74306
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
NUP188-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Sandestig-stefanova syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at