chr12-121022883-T-A

Variant names:

• chr12-121022883-T-A
• rs7957197
• NM_003733.4:c.1047+1107A>T

Variant summary

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

The NM_003733.4(OASL):​c.1047+1107A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,184 control chromosomes in the GnomAD database, including 2,437 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 (2437 hom., cov: 31)
• Consequence: OASL NM_003733.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 143 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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.1047+1107A>T		intron	N/A	NP_003724.1	Q15646-1
	OASL	NM_001261825.2		c.658-1825A>T		intron	N/A	NP_001248754.1	Q15646-3
	OASL	NM_001395419.1		c.1047+1107A>T		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.1047+1107A>T		intron	N/A	ENSP00000257570.4	Q15646-1
	OASL	ENST00000620239.6	TSL:1	c.658-1825A>T		intron	N/A	ENSP00000479512.1	Q15646-3
	OASL	ENST00000339275.10	TSL:1	c.*37+1107A>T		intron	N/A	ENSP00000341125.5	Q15646-2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26435 AN: 152066 Hom.: 2435 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0528

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.174 AC: 26453 AN: 152184 Hom.: 2437 Cov.: 31 AF XY: 0.169 AC XY: 12572 AN XY: 74406

African (AFR) AF: 0.176 AC: 7288 AN: 41522

American (AMR) AF: 0.139 AC: 2118 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5186

South Asian (SAS) AF: 0.0532 AC: 257 AN: 4828

European-Finnish (FIN) AF: 0.221 AC: 2336 AN: 10580

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13161 AN: 67996

Other (OTH) AF: 0.173 AC: 365 AN: 2114

Alfa AF: 0.188 Hom.: 1642

Bravo AF: 0.170

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.86
PhyloP100		0.081
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: rs7957197; hg19: chr12-121460686;