rs10496739

Variant names:

• chr2-135994399-G-A
• rs10496739
• ENST00000419808.5:n.342-4288G>A

Variant summary

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

The ENST00000438432.7(DARS1-AS1):​n.388-4288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 151,818 control chromosomes in the GnomAD database, including 139 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 0.022 (139 hom., cov: 32)
• Consequence: DARS1-AS1 ENST00000438432.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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.342-4288G>A		intron	N/A
	DARS1-AS1	NR_110200.1		n.342-4288G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DARS1-AS1	ENST00000419808.5	TSL:5	n.342-4288G>A		intron	N/A
	DARS1-AS1	ENST00000438432.7	TSL:3	n.388-4288G>A		intron	N/A
	DARS1-AS1	ENST00000446492.1	TSL:3	n.44-4288G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3306 AN: 151700 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.00383

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00819

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0217 AC: 3298 AN: 151818 Hom.: 139 Cov.: 32 AF XY: 0.0261 AC XY: 1939 AN XY: 74172

African (AFR) AF: 0.00382 AC: 158 AN: 41368

American (AMR) AF: 0.0730 AC: 1110 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.0849 AC: 440 AN: 5184

South Asian (SAS) AF: 0.154 AC: 740 AN: 4806

European-Finnish (FIN) AF: 0.0104 AC: 109 AN: 10490

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00821 AC: 558 AN: 67980

Other (OTH) AF: 0.0336 AC: 71 AN: 2110

Alfa AF: 0.0128 Hom.: 63

Bravo AF: 0.0214

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.70
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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: rs10496739;

hg19: chr2-136751969;