rs13311

chr12-113010847-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002535.3(OAS2):c.*1592C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 160,106 control chromosomes in the GnomAD database, including 11,803 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.38 (11226 hom., cov: 30)
  • Exomes 𝑓: 0.32 (577 hom.)
• Consequence: OAS2 NM_002535.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

Genes affected

OAS2 (HGNC:8087): (2'-5'-oligoadenylate synthetase 2) This gene encodes a member of the 2-5A synthetase family, essential proteins involved in the innate immune response to viral infection. The encoded protein is induced by interferons and uses adenosine triphosphate in 2'-specific nucleotidyl transfer reactions to synthesize 2',5'-oligoadenylates (2-5As). These molecules activate latent RNase L, which results in viral RNA degradation and the inhibition of viral replication. The three known members of this gene family are located in a cluster on chromosome 12. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OAS2	NM_002535.3	c.*1592C>A		3_prime_UTR_variant	10/10	ENST00000392583.7
OAS2	NM_016817.3	c.*363C>A		3_prime_UTR_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OAS2	ENST00000392583.7	c.*1592C>A		3_prime_UTR_variant	10/10	1	NM_002535.3	P2
	ENST00000552784.1	n.353+6552G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57796 AN: 151662 Hom.: 11211 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.373

GnomAD4 exome AF: 0.319 AC: 2653 AN: 8326 Hom.: 577 Cov.: 0 AF XY: 0.315 AC XY: 1439 AN XY: 4562

Gnomad4 AFR exome AF: 0.295

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.226

Gnomad4 EAS exome AF: 0.463

Gnomad4 SAS exome AF: 0.352

Gnomad4 FIN exome AF: 0.384

Gnomad4 NFE exome AF: 0.303

Gnomad4 OTH exome AF: 0.325

GnomAD4 genome AF: 0.381 AC: 57853 AN: 151780 Hom.: 11226 Cov.: 30 AF XY: 0.387 AC XY: 28692 AN XY: 74134

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.379

Alfa AF: 0.383 Hom.: 15202

Bravo AF: 0.379

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	8.8
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13311; hg19: chr12-113448652;