chr12-112946950-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006187.4(OAS3):c.844C>A(p.Gln282Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000453 in 1,613,926 control chromosomes in the GnomAD database, including 3 homozygotes. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q282R) has been classified as Uncertain significance.
Frequency
Consequence
NM_006187.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS3 | NM_006187.4 | c.844C>A | p.Gln282Lys | missense_variant | 4/16 | ENST00000228928.12 | |
OAS3 | NM_001410984.1 | c.844C>A | p.Gln282Lys | missense_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS3 | ENST00000228928.12 | c.844C>A | p.Gln282Lys | missense_variant | 4/16 | 1 | NM_006187.4 | P3 | |
ENST00000552784.1 | n.354-38272G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000100 AC: 25AN: 249196Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135190
GnomAD4 exome AF: 0.000491 AC: 717AN: 1461696Hom.: 3 Cov.: 31 AF XY: 0.000503 AC XY: 366AN XY: 727126
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2022 | The c.844C>A (p.Q282K) alteration is located in exon 4 (coding exon 4) of the OAS3 gene. This alteration results from a C to A substitution at nucleotide position 844, causing the glutamine (Q) at amino acid position 282 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at