rs11893318

chr2-135989515-T-Cchr2-135989515-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_110199.1(DARS1-AS1):n.341+3999T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,120 control chromosomes in the GnomAD database, including 3,331 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 (3331 hom., cov: 31)
• Consequence: DARS1-AS1 NR_110199.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DARS1-AS1	NR_110199.1	n.341+3999T>C		intron_variant, non_coding_transcript_variant
DARS1-AS1	NR_110200.1	n.341+3999T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DARS1-AS1	ENST00000692958.1	n.393+3999T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28768 AN: 152002 Hom.: 3327 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.189 AC: 28788 AN: 152120 Hom.: 3331 Cov.: 31 AF XY: 0.196 AC XY: 14595 AN XY: 74360

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.217

Alfa AF: 0.152 Hom.: 1027

Bravo AF: 0.203

Asia WGS AF: 0.285 AC: 989 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	8.7
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11893318; hg19: chr2-136747085;