chr2-136035544-T-C

Variant names:

• chr2-136035544-T-C
• rs4954555
• ENST00000717303.1:n.547+36706T>C

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+36706T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,088 control chromosomes in the GnomAD database, including 4,327 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 0.19 (4327 hom., cov: 32)
• Consequence: DARS1-AS1 ENST00000717303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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+36706T>C		intron	N/A
	DARS1-AS1	ENST00000764009.1		n.542+36706T>C		intron	N/A
	DARS1-AS1	ENST00000764010.1		n.374-42604T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28739 AN: 151970 Hom.: 4313 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.189 AC: 28792 AN: 152088 Hom.: 4327 Cov.: 32 AF XY: 0.195 AC XY: 14494 AN XY: 74360

African (AFR) AF: 0.368 AC: 15268 AN: 41438

American (AMR) AF: 0.215 AC: 3284 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3464

East Asian (EAS) AF: 0.420 AC: 2170 AN: 5170

South Asian (SAS) AF: 0.290 AC: 1398 AN: 4828

European-Finnish (FIN) AF: 0.111 AC: 1175 AN: 10586

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.0626 AC: 4255 AN: 68016

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.112 Hom.: 6300

Bravo AF: 0.207

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.61
DANN	Benign	0.71
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4954555; hg19: chr2-136793114;