chr12-121018070-C-T

Variant names:

• chr12-121018070-C-T
• rs1169279
• ENST00000620239.6:c.*2491G>A

Variant summary

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

The ENST00000620239.6(OASL):​c.*2491G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,024 control chromosomes in the GnomAD database, including 10,005 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 0.35 (10005 hom., cov: 31)
• Consequence: OASL ENST00000620239.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 9 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OASL	NM_001395419.1	c.*907G>A		3_prime_UTR_variant	Exon 6 of 6		NP_001382348.1
OASL	NM_001395418.1	c.*998G>A		3_prime_UTR_variant	Exon 5 of 5		NP_001382347.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OASL	ENST00000620239.6	c.*2491G>A		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000479512.1
OASL	ENST00000680620.1	c.*907G>A		3_prime_UTR_variant	Exon 6 of 6			ENSP00000505685.1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53492 AN: 151906 Hom.: 9994 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.352 AC: 53532 AN: 152024 Hom.: 10005 Cov.: 31 AF XY: 0.360 AC XY: 26777 AN XY: 74320

African (AFR) AF: 0.315 AC: 13065 AN: 41446

American (AMR) AF: 0.380 AC: 5806 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3468

East Asian (EAS) AF: 0.735 AC: 3791 AN: 5160

South Asian (SAS) AF: 0.500 AC: 2412 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3524 AN: 10562

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21897 AN: 67976

Other (OTH) AF: 0.374 AC: 789 AN: 2108

Alfa AF: 0.336 Hom.: 2776

Bravo AF: 0.355

Asia WGS AF: 0.616 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1169279; hg19: chr12-121455873;