2-135988654-G-C

Position:

• chr2-135988654-G-C

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+3138G>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 0.234 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 NR_110199.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DARS1-AS1	NR_110199.1	n.341+3138G>C		intron_variant, non_coding_transcript_variant
DARS1-AS1	NR_110200.1	n.341+3138G>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+3138G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.292

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs309118; hg19: chr2-136746224;