rs2010604

chr12-112970403-G-Cchr12-112970403-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.*430G>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 0.748 in 221,938 control chromosomes in the GnomAD database, including 63,006 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 0.76 (44519 hom., cov: 33)
  • Exomes 𝑓: 0.72 (18487 hom.)
• Consequence: OAS3 NM_006187.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OAS3	NM_006187.4	c.*430G>C		3_prime_UTR_variant	16/16	ENST00000228928.12
OAS3	NM_001410984.1	c.*430G>C		3_prime_UTR_variant	16/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OAS3	ENST00000228928.12	c.*430G>C		3_prime_UTR_variant	16/16	1	NM_006187.4	P3
	ENST00000552784.1	n.353+46996C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115433 AN: 152058 Hom.: 44472 Cov.: 33

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.723

GnomAD4 exome AF: 0.722 AC: 50382 AN: 69762 Hom.: 18487 Cov.: 0 AF XY: 0.723 AC XY: 26218 AN XY: 36242

Gnomad4 AFR exome AF: 0.867

Gnomad4 AMR exome AF: 0.796

Gnomad4 ASJ exome AF: 0.566

Gnomad4 EAS exome AF: 0.916

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.780

Gnomad4 NFE exome AF: 0.689

Gnomad4 OTH exome AF: 0.708

GnomAD4 genome AF: 0.759 AC: 115541 AN: 152176 Hom.: 44519 Cov.: 33 AF XY: 0.765 AC XY: 56914 AN XY: 74394

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.719

Alfa AF: 0.646 Hom.: 1911

Bravo AF: 0.764

Asia WGS AF: 0.824 AC: 2866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.2
Dann	Benign	0.66

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: rs2010604; hg19: chr12-113408208;