rs11513733

chr12-112984508-T-A

Variant summary

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

The NM_002535.3(OAS2):c.178-2530T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0801 in 152,266 control chromosomes in the GnomAD database, including 667 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 0.080 (667 hom., cov: 33)
• Consequence: OAS2 NM_002535.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OAS2	NM_002535.3	c.178-2530T>A		intron_variant		ENST00000392583.7
OAS2	NM_001032731.2	c.178-2530T>A		intron_variant
OAS2	NM_016817.3	c.178-2530T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OAS2	ENST00000392583.7	c.178-2530T>A		intron_variant		1	NM_002535.3	P2
	ENST00000552784.1	n.353+32891A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0802 AC: 12197 AN: 152148 Hom.: 668 Cov.: 33

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0933

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0732

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0801 AC: 12192 AN: 152266 Hom.: 667 Cov.: 33 AF XY: 0.0788 AC XY: 5862 AN XY: 74434

Gnomad4 AFR AF: 0.0204

Gnomad4 AMR AF: 0.0508

Gnomad4 ASJ AF: 0.0933

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0502

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0720

Alfa AF: 0.102 Hom.: 99

Bravo AF: 0.0706

Asia WGS AF: 0.0210 AC: 72 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.6
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: rs11513733; hg19: chr12-113422313;