rs1340000

Positions:

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

Variant summary

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

The ENST00000449643.1(GPR158-AS1):​n.601+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 ENST00000449643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

Genes affected

GPR158-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR158-AS1	NR_027333.2	n.601+3842C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR158-AS1	ENST00000449643.1	n.601+3842C>T		intron_variant		2

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

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.000474

Gnomad4 NFE AF: 0.00537

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0236 Hom.: 57

Bravo AF: 0.0604

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1340000; hg19: chr10-25460763;