2-135988654-G-C

Variant names:

• chr2-135988654-G-C
• rs309118
• ENST00000419808.5:n.341+3138G>C

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+3138G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,974 control chromosomes in the GnomAD database, including 4,833 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 0.23 (4833 hom., cov: 31)
• Consequence: DARS1-AS1 ENST00000438432.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 4 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 = 0.387 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+3138G>C		intron	N/A
	DARS1-AS1	NR_110200.1		n.341+3138G>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+3138G>C		intron	N/A
	DARS1-AS1	ENST00000438432.7	TSL:3	n.387+3138G>C		intron	N/A
	DARS1-AS1	ENST00000446492.1	TSL:3	n.43+3138G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35549 AN: 151856 Hom.: 4814 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.234 AC: 35616 AN: 151974 Hom.: 4833 Cov.: 31 AF XY: 0.239 AC XY: 17726 AN XY: 74314

African (AFR) AF: 0.296 AC: 12237 AN: 41410

American (AMR) AF: 0.259 AC: 3948 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1754 AN: 3472

East Asian (EAS) AF: 0.402 AC: 2073 AN: 5160

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1469 AN: 10572

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11787 AN: 67970

Other (OTH) AF: 0.292 AC: 615 AN: 2104

Alfa AF: 0.214 Hom.: 515

Bravo AF: 0.245

Asia WGS AF: 0.315 AC: 1095 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	0.41
DANN	Benign	0.53
PhyloP100		-0.21

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: rs309118;

hg19: chr2-136746224;