NM_005302.5:c.1024-6317G>A

Variant names:

• chr7-124753660-C-T
• rs2190107
• NM_005302.5:c.1024-6317G>A

Variant summary

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

The NM_005302.5(GPR37):​c.1024-6317G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 151,854 control chromosomes in the GnomAD database, including 1,111 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 0.11 (1111 hom., cov: 32)
• Consequence: GPR37 NM_005302.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 3 publications found

Genes affected

GPR37 (HGNC:4494): (G protein-coupled receptor 37) This gene is a member of the G protein-coupled receptor family. The encoded protein contains seven transmembrane domains and is found in cell and endoplasmic reticulum membranes. G protein-coupled receptors are involved in translating outside signals into G protein mediated intracellular effects. This gene product interacts with Parkin and is involved in juvenile Parkinson disease. [provided by RefSeq, Oct 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005302.5. 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
	GPR37	NM_005302.5	MANE Select	c.1024-6317G>A		intron	N/A	NP_005293.1	O15354

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GPR37	ENST00000303921.3	TSL:1 MANE Select	c.1024-6317G>A		intron	N/A	ENSP00000306449.2	O15354

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16489 AN: 151738 Hom.: 1104 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.0866

Gnomad EAS AF: 0.000774

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.109 AC: 16510 AN: 151854 Hom.: 1111 Cov.: 32 AF XY: 0.109 AC XY: 8119 AN XY: 74232

African (AFR) AF: 0.184 AC: 7621 AN: 41408

American (AMR) AF: 0.0765 AC: 1166 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0866 AC: 300 AN: 3466

East Asian (EAS) AF: 0.000776 AC: 4 AN: 5156

South Asian (SAS) AF: 0.0850 AC: 409 AN: 4814

European-Finnish (FIN) AF: 0.104 AC: 1094 AN: 10546

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0821 AC: 5575 AN: 67908

Other (OTH) AF: 0.104 AC: 220 AN: 2108

Alfa AF: 0.0766 Hom.: 379

Bravo AF: 0.109

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.67
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2190107; hg19: chr7-124393714;