rs6714750

Variant names:

• chr2-136025599-A-G
• rs6714750
• ENST00000717303.1:n.547+26761A>G

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+26761A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,092 control chromosomes in the GnomAD database, including 12,027 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 0.37 (12027 hom., cov: 33)
• Consequence: DARS1-AS1 ENST00000717303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 8 publications found

Genes affected

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

ENSG00000299516 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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.547+26761A>G		intron	N/A
	DARS1-AS1	ENST00000764009.1		n.542+26761A>G		intron	N/A
	DARS1-AS1	ENST00000764010.1		n.373+40078A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56683 AN: 151974 Hom.: 12004 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.373 AC: 56745 AN: 152092 Hom.: 12027 Cov.: 33 AF XY: 0.385 AC XY: 28638 AN XY: 74340

African (AFR) AF: 0.421 AC: 17490 AN: 41498

American (AMR) AF: 0.521 AC: 7971 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3115 AN: 5154

South Asian (SAS) AF: 0.573 AC: 2763 AN: 4824

European-Finnish (FIN) AF: 0.295 AC: 3117 AN: 10570

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18519 AN: 67968

Other (OTH) AF: 0.471 AC: 994 AN: 2112

Alfa AF: 0.324 Hom.: 1877

Bravo AF: 0.389

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	18
DANN	Benign	0.55
PhyloP100		1.5

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: rs6714750;

hg19: chr2-136783169;