2-136062506-C-T

Variant names:

• chr2-136062506-C-T
• rs11681248
• ENST00000717303.1:n.548-15642C>T

Variant summary

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

The ENST00000717303.1(DARS1-AS1):​n.548-15642C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,054 control chromosomes in the GnomAD database, including 16,959 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 0.40 (16959 hom., cov: 32)
• Consequence: DARS1-AS1 ENST00000717303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 5 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 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

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	ENST00000717303.1		n.548-15642C>T		intron	N/A
	DARS1-AS1	ENST00000764009.1		n.543-15642C>T		intron	N/A
	DARS1-AS1	ENST00000764010.1		n.374-15642C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60198 AN: 151936 Hom.: 16960 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.396 AC: 60192 AN: 152054 Hom.: 16959 Cov.: 32 AF XY: 0.384 AC XY: 28565 AN XY: 74332

African (AFR) AF: 0.118 AC: 4895 AN: 41500

American (AMR) AF: 0.253 AC: 3869 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5182

South Asian (SAS) AF: 0.208 AC: 1002 AN: 4822

European-Finnish (FIN) AF: 0.609 AC: 6419 AN: 10538

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42139 AN: 67956

Other (OTH) AF: 0.300 AC: 630 AN: 2102

Alfa AF: 0.494 Hom.: 6129

Bravo AF: 0.358

Asia WGS AF: 0.0880 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.33
PhyloP100		-0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11681248;

hg19: chr2-136820076;