chr10-25412412-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_020752.3(GPR158):c.1274C>G(p.Ala425Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 1,612,848 control chromosomes in the GnomAD database, including 389,197 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_020752.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR158 | NM_020752.3 | c.1274C>G | p.Ala425Gly | missense_variant | 4/11 | ENST00000376351.4 | |
GPR158 | XR_930512.4 | n.1694C>G | non_coding_transcript_exon_variant | 4/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR158 | ENST00000376351.4 | c.1274C>G | p.Ala425Gly | missense_variant | 4/11 | 1 | NM_020752.3 | P2 | |
GPR158 | ENST00000650135.1 | c.1037C>G | p.Ala346Gly | missense_variant | 5/12 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.605 AC: 91930AN: 151926Hom.: 29412 Cov.: 33
GnomAD3 exomes AF: 0.611 AC: 153512AN: 251442Hom.: 50543 AF XY: 0.627 AC XY: 85163AN XY: 135890
GnomAD4 exome AF: 0.692 AC: 1010467AN: 1460804Hom.: 359777 Cov.: 43 AF XY: 0.693 AC XY: 503742AN XY: 726776
GnomAD4 genome ? AF: 0.605 AC: 91971AN: 152044Hom.: 29420 Cov.: 33 AF XY: 0.593 AC XY: 44027AN XY: 74294
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at