chr12-113004991-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002535.3(OAS2):c.1237G>T(p.Val413Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,614,092 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002535.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OAS2 | NM_002535.3 | c.1237G>T | p.Val413Leu | missense_variant | 7/10 | ENST00000392583.7 | |
OAS2 | NM_016817.3 | c.1237G>T | p.Val413Leu | missense_variant | 7/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OAS2 | ENST00000392583.7 | c.1237G>T | p.Val413Leu | missense_variant | 7/10 | 1 | NM_002535.3 | P2 | |
ENST00000552784.1 | n.353+12408C>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251238Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135766
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461870Hom.: 1 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727238
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2021 | The c.1237G>T (p.V413L) alteration is located in exon 7 (coding exon 7) of the OAS2 gene. This alteration results from a G to T substitution at nucleotide position 1237, causing the valine (V) at amino acid position 413 to be replaced by a leucine (L). 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