chr3-98532841-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005290.4(GPR15):c.808C>T(p.Arg270Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. R270Q) has been classified as Likely benign.
Frequency
Consequence
NM_005290.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR15 | NM_005290.4 | c.808C>T | p.Arg270Trp | missense_variant | 1/1 | ENST00000284311.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR15 | ENST00000284311.5 | c.808C>T | p.Arg270Trp | missense_variant | 1/1 | NM_005290.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251298Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135806
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461666Hom.: 0 Cov.: 34 AF XY: 0.0000289 AC XY: 21AN XY: 727082
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.808C>T (p.R270W) alteration is located in exon 1 (coding exon 1) of the GPR15 gene. This alteration results from a C to T substitution at nucleotide position 808, causing the arginine (R) at amino acid position 270 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