rs2011946

Variant names:

• chr2-136060046-C-A
• rs2011946
• ENST00000717303.1:n.548-18102C>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.548-18102C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,146 control chromosomes in the GnomAD database, including 19,655 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 0.45 (19655 hom., cov: 34)
• Consequence: DARS1-AS1 ENST00000717303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 14 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 (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DARS1-AS1	ENST00000717303.1	n.548-18102C>A		intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764009.1	n.543-18102C>A		intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764010.1	n.374-18102C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68582 AN: 152028 Hom.: 19649 Cov.: 34

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.451 AC: 68611 AN: 152146 Hom.: 19655 Cov.: 34 AF XY: 0.441 AC XY: 32772 AN XY: 74392

African (AFR) AF: 0.200 AC: 8303 AN: 41496

American (AMR) AF: 0.305 AC: 4669 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3470

East Asian (EAS) AF: 0.115 AC: 597 AN: 5172

South Asian (SAS) AF: 0.253 AC: 1219 AN: 4824

European-Finnish (FIN) AF: 0.644 AC: 6819 AN: 10592

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44589 AN: 67988

Other (OTH) AF: 0.379 AC: 802 AN: 2116

Alfa AF: 0.564 Hom.: 18497

Bravo AF: 0.418

Asia WGS AF: 0.166 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.15
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2011946; hg19: chr2-136817616;