rs13311

Variant names:

• chr12-113010847-C-A
• rs13311
• NM_002535.3:c.*1592C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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]

ENSG00000257452 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002535.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OAS2	NM_002535.3	MANE Select	c.*1592C>A		3_prime_UTR	Exon 10 of 10	NP_002526.2	P29728-2
	OAS2	NM_016817.3		c.*363C>A		3_prime_UTR	Exon 11 of 11	NP_058197.2	P29728-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OAS2	ENST00000392583.7	TSL:1 MANE Select	c.*1592C>A		3_prime_UTR	Exon 10 of 10	ENSP00000376362.3	P29728-2
	OAS2	ENST00000342315.8	TSL:1	c.*363C>A		3_prime_UTR	Exon 11 of 11	ENSP00000342278.4	P29728-1
	OAS2	ENST00000680122.1		c.*2867C>A		3_prime_UTR	Exon 9 of 9	ENSP00000505194.1	A0A7P0T8H9

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

African (AFR) AF: 0.295 AC: 46 AN: 156

American (AMR) AF: 0.367 AC: 122 AN: 332

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 43 AN: 190

East Asian (EAS) AF: 0.463 AC: 113 AN: 244

South Asian (SAS) AF: 0.352 AC: 279 AN: 792

European-Finnish (FIN) AF: 0.384 AC: 163 AN: 424

Middle Eastern (MID) AF: 0.324 AC: 11 AN: 34

European-Non Finnish (NFE) AF: 0.303 AC: 1725 AN: 5690

Other (OTH) AF: 0.325 AC: 151 AN: 464

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

African (AFR) AF: 0.313 AC: 12954 AN: 41382

American (AMR) AF: 0.457 AC: 6959 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1230 AN: 3466

East Asian (EAS) AF: 0.518 AC: 2662 AN: 5140

South Asian (SAS) AF: 0.455 AC: 2178 AN: 4790

European-Finnish (FIN) AF: 0.427 AC: 4494 AN: 10526

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 25985 AN: 67932

Other (OTH) AF: 0.379 AC: 798 AN: 2108

Alfa AF: 0.379 Hom.: 23052

Bravo AF: 0.379

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.8
DANN	Benign	0.68
PhyloP100		0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13311; hg19: chr12-113448652;