rs2619096

Variant names:

• chr10-117238616-C-T
• rs2619096
• ENST00000425264.2:n.*146G>A

Variant summary

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

The ENST00000425264.2(SLC18A2-AS1):​n.*146G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,964 control chromosomes in the GnomAD database, including 27,289 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 0.57 (27289 hom., cov: 31)
• Consequence: SLC18A2-AS1 ENST00000425264.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

SLC18A2-AS1 (HGNC:55843): (SLC18A2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC18A2-AS1	NR_184309.1	n.*149G>A		downstream_gene_variant
SLC18A2-AS1	NR_184310.1	n.*149G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC18A2-AS1	ENST00000425264.2	n.*146G>A		downstream_gene_variant		3
SLC18A2-AS1	ENST00000691914.2	n.*152G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87283 AN: 151846 Hom.: 27288 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.574 AC: 87284 AN: 151964 Hom.: 27289 Cov.: 31 AF XY: 0.578 AC XY: 42912 AN XY: 74260

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.601

Alfa AF: 0.621 Hom.: 3782

Bravo AF: 0.548

Asia WGS AF: 0.357 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.085

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2619096; hg19: chr10-118998127;