rs2010549

Positions:

• chr12-112971192-G-C
• chr12-112971192-G-T

Variant summary

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

The NM_006187.4(OAS3):​c.*1219G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,312 control chromosomes in the GnomAD database, including 2,857 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 0.18 (2856 hom., cov: 33)
  • Exomes 𝑓: 0.19 (1 hom.)
• Consequence: OAS3 NM_006187.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

OAS3 (HGNC:8088): (2'-5'-oligoadenylate synthetase 3) This gene encodes an enzyme included in the 2', 5' oligoadenylate synthase family. This enzyme is induced by interferons and catalyzes the 2', 5' oligomers of adenosine in order to bind and activate RNase L. This enzyme family plays a significant role in the inhibition of cellular protein synthesis and viral infection resistance. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OAS3	NM_006187.4	c.*1219G>C		3_prime_UTR_variant	16/16	ENST00000228928.12
OAS3	NM_001410984.1	c.*1219G>C		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OAS3	ENST00000228928.12	c.*1219G>C		3_prime_UTR_variant	16/16	1	NM_006187.4	P3
	ENST00000552784.1	n.353+46207C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27569 AN: 152042 Hom.: 2847 Cov.: 33

Gnomad AFR AF: 0.0956

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0832

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.188

GnomAD4 exome AF: 0.191 AC: 29 AN: 152 Hom.: 1 Cov.: 0 AF XY: 0.188 AC XY: 18 AN XY: 96

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.216

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.181 AC: 27610 AN: 152160 Hom.: 2856 Cov.: 33 AF XY: 0.186 AC XY: 13868 AN XY: 74386

Gnomad4 AFR AF: 0.0959

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.0832

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.189

Alfa AF: 0.100 Hom.: 209

Bravo AF: 0.168

Asia WGS AF: 0.298 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.79

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: rs2010549; hg19: chr12-113408997;