12-121018070-C-T

Position:

• chr12-121018070-C-T

Variant summary

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

The NM_001395419.1(OASL):​c.*907G>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 NM_001395419.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
OASL	NM_001395418.1	c.*998G>A		3_prime_UTR_variant	5/5
OASL	NM_001395419.1	c.*907G>A		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OASL	ENST00000680620.1	c.*907G>A		3_prime_UTR_variant	6/6

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

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.374

Alfa AF: 0.340 Hom.: 1663

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1169279; hg19: chr12-121455873;