rs11893318

Variant names:

• chr2-135989515-T-C
• rs11893318
• ENST00000419808.5:n.341+3999T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-135989515-T-C
• chr2-135989515-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438432.7(DARS1-AS1):​n.387+3999T>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 152,120 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 ENST00000438432.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438432.7. 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
	DARS1-AS1	NR_110199.1		n.341+3999T>C		intron	N/A
	DARS1-AS1	NR_110200.1		n.341+3999T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DARS1-AS1	ENST00000419808.5	TSL:5	n.341+3999T>C		intron	N/A
	DARS1-AS1	ENST00000438432.7	TSL:3	n.387+3999T>C		intron	N/A
	DARS1-AS1	ENST00000446492.1	TSL:3	n.43+3999T>C		intron	N/A

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

African (AFR) AF: 0.248 AC: 10294 AN: 41492

American (AMR) AF: 0.306 AC: 4670 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3472

East Asian (EAS) AF: 0.191 AC: 988 AN: 5176

South Asian (SAS) AF: 0.351 AC: 1691 AN: 4824

European-Finnish (FIN) AF: 0.145 AC: 1529 AN: 10562

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8040 AN: 68016

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.151 Hom.: 1147

Bravo AF: 0.203

Asia WGS AF: 0.285 AC: 989 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.7
DANN	Benign	0.37
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism

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: rs11893318;

hg19: chr2-136747085;