chrX-151180141-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004224.3(GPR50):c.558T>C(p.Pro186=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,094,402 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.0000027 ( 0 hom. 1 hem. )
Consequence
GPR50
NM_004224.3 synonymous
NM_004224.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.77
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant X-151180141-T-C is Benign according to our data. Variant chrX-151180141-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2661640.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.77 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR50 | NM_004224.3 | c.558T>C | p.Pro186= | synonymous_variant | 2/2 | ENST00000218316.4 | |
GPR50 | XM_011531216.3 | c.1+49T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR50 | ENST00000218316.4 | c.558T>C | p.Pro186= | synonymous_variant | 2/2 | 1 | NM_004224.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 178842Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65714
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GnomAD4 exome AF: 0.00000274 AC: 3AN: 1094402Hom.: 0 Cov.: 33 AF XY: 0.00000277 AC XY: 1AN XY: 361006
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GnomAD4 genome ? Cov.: 22
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | GPR50: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at