7-124764254-C-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_005302.5(GPR37):​c.723G>T​(p.Thr241Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00808 in 1,598,330 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0062 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0083 ( 64 hom. )

Consequence

GPR37
NM_005302.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -8.33
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 7-124764254-C-A is Benign according to our data. Variant chr7-124764254-C-A is described in ClinVar as [Benign]. Clinvar id is 772891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-8.33 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPR37NM_005302.5 linkc.723G>T p.Thr241Thr synonymous_variant Exon 1 of 2 ENST00000303921.3 NP_005293.1 O15354

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPR37ENST00000303921.3 linkc.723G>T p.Thr241Thr synonymous_variant Exon 1 of 2 1 NM_005302.5 ENSP00000306449.2 O15354

Frequencies

GnomAD3 genomes
AF:
0.00622
AC:
946
AN:
152176
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00133
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00242
Gnomad ASJ
AF:
0.00663
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00310
Gnomad FIN
AF:
0.00631
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0109
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00660
AC:
1565
AN:
237134
Hom.:
16
AF XY:
0.00653
AC XY:
833
AN XY:
127608
show subpopulations
Gnomad AFR exome
AF:
0.00130
Gnomad AMR exome
AF:
0.00140
Gnomad ASJ exome
AF:
0.00735
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00261
Gnomad FIN exome
AF:
0.00491
Gnomad NFE exome
AF:
0.0114
Gnomad OTH exome
AF:
0.00494
GnomAD4 exome
AF:
0.00828
AC:
11977
AN:
1446036
Hom.:
64
Cov.:
31
AF XY:
0.00822
AC XY:
5900
AN XY:
717778
show subpopulations
Gnomad4 AFR exome
AF:
0.00118
Gnomad4 AMR exome
AF:
0.00146
Gnomad4 ASJ exome
AF:
0.00761
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.00245
Gnomad4 FIN exome
AF:
0.00602
Gnomad4 NFE exome
AF:
0.00978
Gnomad4 OTH exome
AF:
0.00594
GnomAD4 genome
AF:
0.00621
AC:
945
AN:
152294
Hom.:
5
Cov.:
32
AF XY:
0.00585
AC XY:
436
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.00132
Gnomad4 AMR
AF:
0.00242
Gnomad4 ASJ
AF:
0.00663
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00311
Gnomad4 FIN
AF:
0.00631
Gnomad4 NFE
AF:
0.0109
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00848
Hom.:
2
Bravo
AF:
0.00560
Asia WGS
AF:
0.00375
AC:
13
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Jul 10, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.20
DANN
Benign
0.39

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs62638683; hg19: chr7-124404308; API