rs932206

Variant names:

• chr2-136067702-C-T
• rs932206
• ENST00000717303.1:n.548-10446C>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.548-10446C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,084 control chromosomes in the GnomAD database, including 13,205 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 0.35 (13205 hom., cov: 32)
• Consequence: DARS1-AS1 ENST00000717303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 17 publications found

Genes affected

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

ENSG00000299532 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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.548-10446C>T		intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764009.1	n.543-10446C>T		intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764010.1	n.374-10446C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53187 AN: 151966 Hom.: 13206 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.350 AC: 53180 AN: 152084 Hom.: 13205 Cov.: 32 AF XY: 0.337 AC XY: 25069 AN XY: 74342

African (AFR) AF: 0.107 AC: 4422 AN: 41512

American (AMR) AF: 0.235 AC: 3584 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3468

East Asian (EAS) AF: 0.00250 AC: 13 AN: 5192

South Asian (SAS) AF: 0.190 AC: 915 AN: 4818

European-Finnish (FIN) AF: 0.491 AC: 5178 AN: 10546

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37317 AN: 67956

Other (OTH) AF: 0.269 AC: 570 AN: 2116

Alfa AF: 0.463 Hom.: 9255

Bravo AF: 0.321

Asia WGS AF: 0.0860 AC: 300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.74
DANN	Benign	0.44
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs932206; hg19: chr2-136825272;