rs1340000

Variant names:

• chr10-25171834-G-A
• rs1340000
• ENST00000449643.2:n.1032+3842C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-25171834-G-A
• chr10-25171834-G-T

Variant summary

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

The ENST00000449643.2(GPR158-AS1):​n.1032+3842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 151,970 control chromosomes in the GnomAD database, including 570 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 0.053 (570 hom., cov: 33)
• Consequence: GPR158-AS1 ENST00000449643.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 1 publications found

Genes affected

GPR158-AS1 (HGNC:44163): (GPR158 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449643.2. 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
	GPR158-AS1	NR_027333.2		n.601+3842C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR158-AS1	ENST00000449643.2	TSL:2	n.1032+3842C>T		intron	N/A
	GPR158-AS1	ENST00000808924.1		n.886+3605C>T		intron	N/A
	GPR158-AS1	ENST00000808925.1		n.251+4603C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 8045 AN: 151852 Hom.: 566 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0384

Gnomad FIN AF: 0.000474

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.00537

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0531 AC: 8076 AN: 151970 Hom.: 570 Cov.: 33 AF XY: 0.0526 AC XY: 3910 AN XY: 74284

African (AFR) AF: 0.165 AC: 6838 AN: 41408

American (AMR) AF: 0.0355 AC: 541 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.00547 AC: 19 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.0380 AC: 183 AN: 4814

European-Finnish (FIN) AF: 0.000474 AC: 5 AN: 10552

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.00537 AC: 365 AN: 67980

Other (OTH) AF: 0.0497 AC: 105 AN: 2114

Alfa AF: 0.0265 Hom.: 67

Bravo AF: 0.0604

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-0.045
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1340000; hg19: chr10-25460763;