12-112997634-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002535.3(OAS2):c.742G>A(p.Val248Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000731 in 1,614,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002535.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000116 AC: 29AN: 251074Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135676
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727222
GnomAD4 genome AF: 0.000368 AC: 56AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74474
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at