rs749873

Variant names:

• chr2-136059518-C-T
• rs749873
• ENST00000717303.1:n.548-18630C>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.548-18630C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,502 control chromosomes in the GnomAD database, including 17,578 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 0.41 (17578 hom., cov: 30)
• Consequence: DARS1-AS1 ENST00000717303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 12 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=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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.548-18630C>T		intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764009.1	n.543-18630C>T		intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764010.1	n.374-18630C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61692 AN: 151386 Hom.: 17582 Cov.: 30

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0286

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.407 AC: 61683 AN: 151502 Hom.: 17578 Cov.: 30 AF XY: 0.395 AC XY: 29261 AN XY: 74012

African (AFR) AF: 0.120 AC: 4972 AN: 41368

American (AMR) AF: 0.271 AC: 4137 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3464

East Asian (EAS) AF: 0.0287 AC: 148 AN: 5162

South Asian (SAS) AF: 0.215 AC: 1035 AN: 4810

European-Finnish (FIN) AF: 0.617 AC: 6370 AN: 10316

Middle Eastern (MID) AF: 0.128 AC: 37 AN: 290

European-Non Finnish (NFE) AF: 0.633 AC: 42971 AN: 67836

Other (OTH) AF: 0.317 AC: 667 AN: 2106

Alfa AF: 0.526 Hom.: 79127

Bravo AF: 0.369

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs749873; hg19: chr2-136817088;