chrX-151176819-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004224.3(GPR50):āc.98G>Cā(p.Cys33Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000667 in 1,199,941 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 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 (ā ).
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.98G>C | p.Cys33Ser | missense_variant | 1/2 | ENST00000218316.4 | |
GPR50-AS1 | NR_135300.1 | n.517C>G | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR50 | ENST00000218316.4 | c.98G>C | p.Cys33Ser | missense_variant | 1/2 | 1 | NM_004224.3 | P1 | |
GPR50-AS1 | ENST00000454196.1 | n.517C>G | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000901 AC: 1AN: 110973Hom.: 0 Cov.: 23 AF XY: 0.0000301 AC XY: 1AN XY: 33213
GnomAD3 exomes AF: 0.0000111 AC: 2AN: 180445Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66373
GnomAD4 exome AF: 0.00000643 AC: 7AN: 1088968Hom.: 0 Cov.: 28 AF XY: 0.0000113 AC XY: 4AN XY: 354922
GnomAD4 genome AF: 0.00000901 AC: 1AN: 110973Hom.: 0 Cov.: 23 AF XY: 0.0000301 AC XY: 1AN XY: 33213
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2023 | The c.98G>C (p.C33S) alteration is located in exon 1 (coding exon 1) of the GPR50 gene. This alteration results from a G to C substitution at nucleotide position 98, causing the cysteine (C) at amino acid position 33 to be replaced by a serine (S). 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