rs7520258

chr1-236149827-T-C

Variant summary

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

The NM_003272.4(GPR137B):c.414+6791T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,326 control chromosomes in the GnomAD database, including 854 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 0.071 (854 hom., cov: 34)
• Consequence: GPR137B NM_003272.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

Genes affected

GPR137B (HGNC:11862): (G protein-coupled receptor 137B) Involved in several processes, including positive regulation of TORC1 signaling; positive regulation of protein localization to lysosome; and regulation of GTPase activity. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPR137B	NM_003272.4	c.414+6791T>C		intron_variant		ENST00000366592.8
GPR137B	XM_017002209.3	c.414+6791T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPR137B	ENST00000366592.8	c.414+6791T>C		intron_variant		1	NM_003272.4	P1
GPR137B	ENST00000419162.5	c.414+6791T>C		intron_variant, NMD_transcript_variant		5
GPR137B	ENST00000366591.4	n.493+6791T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0706 AC: 10739 AN: 152210 Hom.: 850 Cov.: 34

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.00423

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00951

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0707 AC: 10762 AN: 152326 Hom.: 854 Cov.: 34 AF XY: 0.0720 AC XY: 5367 AN XY: 74496

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0561

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.00423

Gnomad4 NFE AF: 0.00951

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0271 Hom.: 311

Bravo AF: 0.0828

Asia WGS AF: 0.140 AC: 486 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.82
Dann	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7520258; hg19: chr1-236313127;