2-136008381-T-C

Variant names:

• chr2-136008381-T-C
• rs309137
• ENST00000399447.7:n.456-486T>C

Variant summary

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

The ENST00000669983.1(DARS1-AS1):​n.370-8077T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,958 control chromosomes in the GnomAD database, including 24,761 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 0.52 (24761 hom., cov: 31)
• Consequence: DARS1-AS1 ENST00000669983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 24 publications found

Genes affected

DARS1-AS1 (HGNC:40170): (DARS1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669983.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DARS1-AS1	ENST00000399447.7	TSL:5	n.456-486T>C		intron	N/A
	DARS1-AS1	ENST00000419808.5	TSL:5	n.494-486T>C		intron	N/A
	DARS1-AS1	ENST00000593405.5	TSL:5	n.68-4469T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78336 AN: 151840 Hom.: 24704 Cov.: 31

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.516 AC: 78450 AN: 151958 Hom.: 24761 Cov.: 31 AF XY: 0.526 AC XY: 39058 AN XY: 74270

African (AFR) AF: 0.822 AC: 34088 AN: 41466

American (AMR) AF: 0.611 AC: 9313 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2561 AN: 3468

East Asian (EAS) AF: 0.684 AC: 3524 AN: 5152

South Asian (SAS) AF: 0.651 AC: 3133 AN: 4814

European-Finnish (FIN) AF: 0.335 AC: 3533 AN: 10562

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20625 AN: 67930

Other (OTH) AF: 0.580 AC: 1224 AN: 2110

Alfa AF: 0.438 Hom.: 32421

Bravo AF: 0.548

Asia WGS AF: 0.630 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.46
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs309137; hg19: chr2-136765951; COSMIC: COSV68093956;