chr12-112948031-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006187.4(OAS3):c.961G>A(p.Ala321Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000563 in 1,599,968 control chromosomes in the GnomAD database, including 2 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 (★).
Frequency
Consequence
NM_006187.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS3 | NM_006187.4 | c.961G>A | p.Ala321Thr | missense_variant | 5/16 | ENST00000228928.12 | |
OAS3 | NM_001410984.1 | c.961G>A | p.Ala321Thr | missense_variant | 5/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS3 | ENST00000228928.12 | c.961G>A | p.Ala321Thr | missense_variant | 5/16 | 1 | NM_006187.4 | P3 | |
ENST00000552784.1 | n.354-39353C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000894 AC: 21AN: 234784Hom.: 0 AF XY: 0.000118 AC XY: 15AN XY: 127496
GnomAD4 exome AF: 0.0000601 AC: 87AN: 1447740Hom.: 2 Cov.: 30 AF XY: 0.0000959 AC XY: 69AN XY: 719396
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.961G>A (p.A321T) alteration is located in exon 5 (coding exon 5) of the OAS3 gene. This alteration results from a G to A substitution at nucleotide position 961, causing the alanine (A) at amino acid position 321 to be replaced by a threonine (T). 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