12-112961114-G-A

Variant names:

• chr12-112961114-G-A
• rs2072136
• NM_006187.4:c.1701G>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_006187.4(OAS3):​c.1701G>A​(p.Ser567Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,612,810 control chromosomes in the GnomAD database, including 58,973 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. Synonymous variant affecting the same amino acid position (i.e. S567S) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.23 (5145 hom., cov: 33)
  • Exomes 𝑓: 0.26 (53828 hom.)
• Consequence: OAS3 NM_006187.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 32 publications found

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]

ENSG00000257452 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=-1.11 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006187.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OAS3	NM_006187.4	MANE Select	c.1701G>A	p.Ser567Ser	synonymous	Exon 8 of 16	NP_006178.2
	OAS3	NM_001410984.1		c.1701G>A	p.Ser567Ser	synonymous	Exon 8 of 16	NP_001397913.1	A0A7P0T8S7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OAS3	ENST00000228928.12	TSL:1 MANE Select	c.1701G>A	p.Ser567Ser	synonymous	Exon 8 of 16	ENSP00000228928.7	Q9Y6K5
	OAS3	ENST00000679493.1		c.1701G>A	p.Ser567Ser	synonymous	Exon 8 of 16	ENSP00000506397.1	A0A7P0TAU8
	OAS3	ENST00000681346.1		c.1701G>A	p.Ser567Ser	synonymous	Exon 8 of 17	ENSP00000505939.1	A0A7P0Z4F1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35348 AN: 151598 Hom.: 5138 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.234

GnomAD2 exomes AF: 0.307 AC: 76067 AN: 248092 AF XY: 0.304

Gnomad AFR exome AF: 0.106

Gnomad AMR exome AF: 0.387

Gnomad ASJ exome AF: 0.155

Gnomad EAS exome AF: 0.669

Gnomad FIN exome AF: 0.375

Gnomad NFE exome AF: 0.237

Gnomad OTH exome AF: 0.261

GnomAD4 exome AF: 0.256 AC: 373939 AN: 1461094 Hom.: 53828 Cov.: 35 AF XY: 0.259 AC XY: 188293 AN XY: 726790

African (AFR) AF: 0.0973 AC: 3256 AN: 33462

American (AMR) AF: 0.369 AC: 16442 AN: 44598

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 4097 AN: 26126

East Asian (EAS) AF: 0.648 AC: 25711 AN: 39674

South Asian (SAS) AF: 0.372 AC: 32036 AN: 86174

European-Finnish (FIN) AF: 0.373 AC: 19897 AN: 53352

Middle Eastern (MID) AF: 0.180 AC: 1038 AN: 5766

European-Non Finnish (NFE) AF: 0.231 AC: 256575 AN: 1111590

Other (OTH) AF: 0.247 AC: 14887 AN: 60352

GnomAD4 genome AF: 0.233 AC: 35367 AN: 151716 Hom.: 5145 Cov.: 33 AF XY: 0.245 AC XY: 18141 AN XY: 74150

African (AFR) AF: 0.110 AC: 4513 AN: 41076

American (AMR) AF: 0.276 AC: 4215 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 491 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3400 AN: 5174

South Asian (SAS) AF: 0.383 AC: 1845 AN: 4820

European-Finnish (FIN) AF: 0.372 AC: 3933 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16343 AN: 68000

Other (OTH) AF: 0.234 AC: 493 AN: 2104

Alfa AF: 0.226 Hom.: 6739

Bravo AF: 0.218

Asia WGS AF: 0.428 AC: 1485 AN: 3478

EpiCase AF: 0.219

EpiControl AF: 0.210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2072136; hg19: chr12-113398919; COSMIC: COSV57449812; COSMIC: COSV57449812;