rs1131454
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016816.4(OAS1):c.484G>A(p.Gly162Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,612,274 control chromosomes in the GnomAD database, including 259,474 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 Benign (★★).
Frequency
Consequence
NM_016816.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS1 | NM_016816.4 | c.484G>A | p.Gly162Ser | missense_variant | 3/6 | ENST00000202917.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS1 | ENST00000202917.10 | c.484G>A | p.Gly162Ser | missense_variant | 3/6 | 1 | NM_016816.4 | P2 | |
ENST00000552784.1 | n.354-2387C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.486 AC: 73719AN: 151706Hom.: 20085 Cov.: 30
GnomAD3 exomes AF: 0.569 AC: 142536AN: 250300Hom.: 42483 AF XY: 0.571 AC XY: 77277AN XY: 135218
GnomAD4 exome AF: 0.567 AC: 828699AN: 1460450Hom.: 239378 Cov.: 43 AF XY: 0.568 AC XY: 412896AN XY: 726498
GnomAD4 genome ? AF: 0.486 AC: 73751AN: 151824Hom.: 20096 Cov.: 30 AF XY: 0.494 AC XY: 36626AN XY: 74184
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | This variant is associated with the following publications: (PMID: 16014697) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
OAS1 polymorphism Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Feb 01, 2006 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 87% of patients studied by a panel of primary immunodeficiencies. Number of patients: 83. Only high quality variants are reported. - |
OAS1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 17, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at