rs12811390

Variant names:

• chr12-121032217-C-T
• rs12811390
• NM_003733.4:c.482-600G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003733.4(OASL):​c.482-600G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 151,930 control chromosomes in the GnomAD database, including 1,859 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 0.14 (1859 hom., cov: 31)
• Consequence: OASL NM_003733.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 5 publications found

Genes affected

OASL (HGNC:8090): (2'-5'-oligoadenylate synthetase like) Enables DNA binding activity and double-stranded RNA binding activity. Involved in several processes, including interleukin-27-mediated signaling pathway; negative regulation of viral genome replication; and positive regulation of RIG-I signaling pathway. Located in cytosol; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003733.4. 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
	OASL	NM_003733.4	MANE Select	c.482-600G>A		intron	N/A	NP_003724.1	Q15646-1
	OASL	NM_001261825.2		c.482-600G>A		intron	N/A	NP_001248754.1	Q15646-3
	OASL	NM_001395419.1		c.482-600G>A		intron	N/A	NP_001382348.1	A0A7P0T9H8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OASL	ENST00000257570.10	TSL:1 MANE Select	c.482-600G>A		intron	N/A	ENSP00000257570.4	Q15646-1
	OASL	ENST00000620239.6	TSL:1	c.482-600G>A		intron	N/A	ENSP00000479512.1	Q15646-3
	OASL	ENST00000339275.10	TSL:1	c.482-600G>A		intron	N/A	ENSP00000341125.5	Q15646-2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21885 AN: 151812 Hom.: 1858 Cov.: 31

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.121

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 21894 AN: 151930 Hom.: 1859 Cov.: 31 AF XY: 0.146 AC XY: 10854 AN XY: 74260

African (AFR) AF: 0.0694 AC: 2879 AN: 41464

American (AMR) AF: 0.107 AC: 1627 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3468

East Asian (EAS) AF: 0.120 AC: 618 AN: 5146

South Asian (SAS) AF: 0.157 AC: 757 AN: 4810

European-Finnish (FIN) AF: 0.204 AC: 2149 AN: 10534

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12953 AN: 67934

Other (OTH) AF: 0.120 AC: 254 AN: 2114

Alfa AF: 0.177 Hom.: 354

Bravo AF: 0.130

Asia WGS AF: 0.0960 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.84
PhyloP100		0.56
Mutation Taster		=100/0	polymorphism (auto)

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: rs12811390; hg19: chr12-121470020;