chrX-151180091-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004224.3(GPR50):c.508G>A(p.Glu170Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,208,257 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 72 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004224.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR50 | NM_004224.3 | c.508G>A | p.Glu170Lys | missense_variant | 2/2 | ENST00000218316.4 | |
GPR50 | XM_011531216.3 | c.-1G>A | splice_region_variant, 5_prime_UTR_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR50 | ENST00000218316.4 | c.508G>A | p.Glu170Lys | missense_variant | 2/2 | 1 | NM_004224.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000117 AC: 13AN: 111204Hom.: 0 Cov.: 23 AF XY: 0.000120 AC XY: 4AN XY: 33426
GnomAD3 exomes AF: 0.000127 AC: 23AN: 181214Hom.: 0 AF XY: 0.0000746 AC XY: 5AN XY: 66984
GnomAD4 exome AF: 0.000192 AC: 211AN: 1097053Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 68AN XY: 362481
GnomAD4 genome AF: 0.000117 AC: 13AN: 111204Hom.: 0 Cov.: 23 AF XY: 0.000120 AC XY: 4AN XY: 33426
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.508G>A (p.E170K) alteration is located in exon 2 (coding exon 2) of the GPR50 gene. This alteration results from a G to A substitution at nucleotide position 508, causing the glutamic acid (E) at amino acid position 170 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at