12-112971455-T-C

Position:

• chr12-112971455-T-C

Variant summary

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

The NM_006187.4(OAS3):​c.*1482T>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 0.173 in 152,514 control chromosomes in the GnomAD database, including 2,418 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 0.17 (2414 hom., cov: 33)
  • Exomes 𝑓: 0.21 (4 hom.)
• Consequence: OAS3 NM_006187.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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]

OAS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OAS3	NM_006187.4	c.*1482T>C		3_prime_UTR_variant	16/16	ENST00000228928.12	NP_006178.2
OAS3	NM_001410984.1	c.*1482T>C		3_prime_UTR_variant	16/16		NP_001397913.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OAS3	ENST00000228928.12	c.*1482T>C		3_prime_UTR_variant	16/16	1	NM_006187.4	ENSP00000228928.7

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26291 AN: 152070 Hom.: 2417 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.215 AC: 70 AN: 326 Hom.: 4 Cov.: 0 AF XY: 0.234 AC XY: 44 AN XY: 188

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.286

Gnomad4 EAS exome AF: 0.227

Gnomad4 FIN exome AF: 0.269

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.173 AC: 26297 AN: 152188 Hom.: 2414 Cov.: 33 AF XY: 0.176 AC XY: 13073 AN XY: 74392

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.183

Alfa AF: 0.185 Hom.: 5110

Bravo AF: 0.171

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.67

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: rs2072133; hg19: chr12-113409260;