rs28384811
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003036.4(SKI):āc.185C>Gā(p.Ala62Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 1,396,788 control chromosomes in the GnomAD database, including 3,804 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A62S) has been classified as Uncertain significance.
Frequency
Consequence
NM_003036.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0533 AC: 8011AN: 150266Hom.: 290 Cov.: 32
GnomAD3 exomes AF: 0.0877 AC: 4816AN: 54924Hom.: 263 AF XY: 0.0899 AC XY: 2971AN XY: 33050
GnomAD4 exome AF: 0.0724 AC: 90238AN: 1246414Hom.: 3514 Cov.: 32 AF XY: 0.0737 AC XY: 45257AN XY: 614398
GnomAD4 genome AF: 0.0533 AC: 8009AN: 150374Hom.: 290 Cov.: 32 AF XY: 0.0510 AC XY: 3746AN XY: 73436
ClinVar
Submissions by phenotype
not specified Benign:5
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Ala62Gly in exon 1 of SKI: This variant is not expected to have clinical signifi cance because it has been identified in 10.6% (14/132) of Mexican chromosomes fr om a broad population by the 1000 Genomes Project (http://www.ncbi.nlm.nih.gov/p rojects/SNP; dbSNP rs28384811). -
not provided Benign:3
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Shprintzen-Goldberg syndrome Benign:3
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Familial thoracic aortic aneurysm and aortic dissection Benign:1
This alteration is classified as 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at