X-151181061-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004224.3(GPR50):c.1478G>A(p.Ser493Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0822 in 1,208,046 control chromosomes in the GnomAD database, including 3,041 homozygotes. There are 32,046 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004224.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR50 | NM_004224.3 | c.1478G>A | p.Ser493Asn | missense_variant | 2/2 | ENST00000218316.4 | |
GPR50 | XM_011531216.3 | c.737G>A | p.Ser246Asn | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR50 | ENST00000218316.4 | c.1478G>A | p.Ser493Asn | missense_variant | 2/2 | 1 | NM_004224.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0965 AC: 10634AN: 110177Hom.: 420 Cov.: 22 AF XY: 0.0886 AC XY: 2878AN XY: 32497
GnomAD3 exomes AF: 0.0793 AC: 14359AN: 181112Hom.: 396 AF XY: 0.0792 AC XY: 5309AN XY: 67072
GnomAD4 exome AF: 0.0808 AC: 88711AN: 1097810Hom.: 2621 Cov.: 34 AF XY: 0.0802 AC XY: 29151AN XY: 363324
GnomAD4 genome AF: 0.0966 AC: 10649AN: 110236Hom.: 420 Cov.: 22 AF XY: 0.0889 AC XY: 2895AN XY: 32564
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at