chr10-25466657-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020752.3(GPR158):c.1342C>T(p.Arg448Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000562 in 1,600,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R448Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020752.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR158 | NM_020752.3 | c.1342C>T | p.Arg448Trp | missense_variant | 5/11 | ENST00000376351.4 | |
GPR158 | XM_017016452.3 | c.-219C>T | 5_prime_UTR_variant | 2/8 | |||
GPR158 | XR_930512.4 | n.1762C>T | non_coding_transcript_exon_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR158 | ENST00000376351.4 | c.1342C>T | p.Arg448Trp | missense_variant | 5/11 | 1 | NM_020752.3 | P2 | |
GPR158 | ENST00000650135.1 | c.1105C>T | p.Arg369Trp | missense_variant | 6/12 | A2 | |||
GPR158 | ENST00000482641.2 | n.176C>T | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152118Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000106 AC: 26AN: 246272Hom.: 0 AF XY: 0.0000601 AC XY: 8AN XY: 133078
GnomAD4 exome AF: 0.0000359 AC: 52AN: 1448200Hom.: 0 Cov.: 27 AF XY: 0.0000333 AC XY: 24AN XY: 720096
GnomAD4 genome ? AF: 0.000250 AC: 38AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1342C>T (p.R448W) alteration is located in exon 5 (coding exon 5) of the GPR158 gene. This alteration results from a C to T substitution at nucleotide position 1342, causing the arginine (R) at amino acid position 448 to be replaced by a tryptophan (W). 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