rs2240185

Variant names:

• chr12-113006312-C-A
• rs2240185
• NM_002535.3:c.1469-101C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-113006312-C-A
• chr12-113006312-C-G
• chr12-113006312-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002535.3(OAS2):​c.1469-101C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000012 in 830,604 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000012 (0 hom.)
• Consequence: OAS2 NM_002535.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OAS2	NM_002535.3	MANE Select	c.1469-101C>A		intron	N/A	NP_002526.2
	OAS2	NM_016817.3		c.1469-101C>A		intron	N/A	NP_058197.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OAS2	ENST00000392583.7	TSL:1 MANE Select	c.1469-101C>A		intron	N/A	ENSP00000376362.3
	OAS2	ENST00000342315.8	TSL:1	c.1469-101C>A		intron	N/A	ENSP00000342278.4
	OAS2	ENST00000620097.2	TSL:5	c.1361-101C>A		intron	N/A	ENSP00000483679.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000120 AC: 1 AN: 830604 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 411418

African (AFR) AF: 0.00 AC: 0 AN: 19956

American (AMR) AF: 0.00 AC: 0 AN: 19322

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14832

East Asian (EAS) AF: 0.00 AC: 0 AN: 32730

South Asian (SAS) AF: 0.00 AC: 0 AN: 39876

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40886

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2560

European-Non Finnish (NFE) AF: 0.00000160 AC: 1 AN: 623322

Other (OTH) AF: 0.00 AC: 0 AN: 37120

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.099
PhyloP100		-0.35

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: rs2240185; hg19: chr12-113444117;