7-124744273-G-T

Variant names:

• chr7-124744273-G-T
• rs7802263
• NM_005302.5:c.*2252C>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.*2252C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,936 control chromosomes in the GnomAD database, including 38,876 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 0.70 (38873 hom., cov: 31)
  • Exomes 𝑓: 0.70 (3 hom.)
• Consequence: GPR37 NM_005302.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 6 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]

ENSG00000279419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPR37	NM_005302.5	c.*2252C>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000303921.3	NP_005293.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPR37	ENST00000303921.3	c.*2252C>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_005302.5	ENSP00000306449.2
ENSG00000279419	ENST00000624256.1	n.745C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106707 AN: 151808 Hom.: 38843 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.732

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 3 Cov.: 0 AF XY: 0.625 AC XY: 5 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.700 AC: 7 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.703 AC: 106785 AN: 151926 Hom.: 38873 Cov.: 31 AF XY: 0.707 AC XY: 52492 AN XY: 74260

African (AFR) AF: 0.500 AC: 20710 AN: 41388

American (AMR) AF: 0.805 AC: 12273 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2696 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5168 AN: 5180

South Asian (SAS) AF: 0.811 AC: 3914 AN: 4824

European-Finnish (FIN) AF: 0.762 AC: 8045 AN: 10558

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51462 AN: 67934

Other (OTH) AF: 0.736 AC: 1556 AN: 2114

Alfa AF: 0.742 Hom.: 25507

Bravo AF: 0.699

Asia WGS AF: 0.892 AC: 3101 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	0.068
DANN	Benign	0.27
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7802263; hg19: chr7-124384327;