2-136034846-G-A

Variant names:

• chr2-136034846-G-A
• rs1469816
• ENST00000717303.1:n.547+36008G>A

Variant summary

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

The ENST00000717303.1(DARS1-AS1):​n.547+36008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 151,980 control chromosomes in the GnomAD database, including 1,681 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 0.096 (1681 hom., cov: 32)
• Consequence: DARS1-AS1 ENST00000717303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717303.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DARS1-AS1	ENST00000717303.1		n.547+36008G>A		intron	N/A
	DARS1-AS1	ENST00000764009.1		n.542+36008G>A		intron	N/A
	DARS1-AS1	ENST00000764010.1		n.374-43302G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14533 AN: 151862 Hom.: 1675 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0498

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0234

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0175

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.0959 AC: 14569 AN: 151980 Hom.: 1681 Cov.: 32 AF XY: 0.0948 AC XY: 7042 AN XY: 74288

African (AFR) AF: 0.270 AC: 11172 AN: 41392

American (AMR) AF: 0.0497 AC: 758 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.120 AC: 623 AN: 5172

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4826

European-Finnish (FIN) AF: 0.0234 AC: 247 AN: 10578

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0175 AC: 1189 AN: 67978

Other (OTH) AF: 0.0843 AC: 177 AN: 2100

Alfa AF: 0.0726 Hom.: 172

Bravo AF: 0.108

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.45
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs1469816; hg19: chr2-136792416;