X-151176899-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP3BP6_Very_StrongBS2
The NM_004224.3(GPR50):c.178C>T(p.Arg60Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000398 in 1,197,034 control chromosomes in the GnomAD database, including 1 homozygotes. There are 144 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., 4 hem., cov: 22)
Exomes 𝑓: 0.00042 ( 1 hom. 140 hem. )
Consequence
GPR50
NM_004224.3 missense
NM_004224.3 missense
Scores
5
9
3
Clinical Significance
Conservation
PhyloP100: 1.35
Genes affected
GPR50 (HGNC:4506): (G protein-coupled receptor 50) This gene product belongs to the G-protein coupled receptor 1 family. Even though this protein shares similarity with the melatonin receptors, it does not bind melatonin, however, it inhibits melatonin receptor 1A function through heterodimerization. Polymorphic variants of this gene have been associated with bipolar affective disorder in women. [provided by RefSeq, Jan 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.791
BP6
Variant X-151176899-C-T is Benign according to our data. Variant chrX-151176899-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1206241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-151176899-C-T is described in Lovd as [Likely_benign].
BS2
High Hemizygotes in GnomAd4 at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR50 | NM_004224.3 | c.178C>T | p.Arg60Trp | missense_variant | 1/2 | ENST00000218316.4 | NP_004215.2 | |
GPR50-AS1 | NR_135300.1 | n.461-24G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR50 | ENST00000218316.4 | c.178C>T | p.Arg60Trp | missense_variant | 1/2 | 1 | NM_004224.3 | ENSP00000218316.3 | ||
GPR50-AS1 | ENST00000454196.1 | n.461-24G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 22AN: 111452Hom.: 0 Cov.: 22 AF XY: 0.000119 AC XY: 4AN XY: 33632
GnomAD3 genomes
AF:
AC:
22
AN:
111452
Hom.:
Cov.:
22
AF XY:
AC XY:
4
AN XY:
33632
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000301 AC: 52AN: 172622Hom.: 0 AF XY: 0.000321 AC XY: 19AN XY: 59128
GnomAD3 exomes
AF:
AC:
52
AN:
172622
Hom.:
AF XY:
AC XY:
19
AN XY:
59128
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000418 AC: 454AN: 1085582Hom.: 1 Cov.: 27 AF XY: 0.000398 AC XY: 140AN XY: 351700
GnomAD4 exome
AF:
AC:
454
AN:
1085582
Hom.:
Cov.:
27
AF XY:
AC XY:
140
AN XY:
351700
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000197 AC: 22AN: 111452Hom.: 0 Cov.: 22 AF XY: 0.000119 AC XY: 4AN XY: 33632
GnomAD4 genome
AF:
AC:
22
AN:
111452
Hom.:
Cov.:
22
AF XY:
AC XY:
4
AN XY:
33632
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
0
ESP6500EA
AF:
AC:
2
ExAC
AF:
AC:
40
ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | GPR50: BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
D
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
MutationAssessor
Pathogenic
H
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at