13-99255097-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001098200.2(GPR18):c.776C>T(p.Thr259Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,614,054 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 (★).
Frequency
Consequence
NM_001098200.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR18 | NM_001098200.2 | c.776C>T | p.Thr259Met | missense_variant | 2/2 | ENST00000397470.5 | NP_001091670.1 | |
UBAC2 | NM_001144072.2 | c.389+10473G>A | intron_variant | ENST00000403766.8 | NP_001137544.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR18 | ENST00000397470.5 | c.776C>T | p.Thr259Met | missense_variant | 2/2 | 1 | NM_001098200.2 | ENSP00000380610.2 | ||
UBAC2 | ENST00000403766.8 | c.389+10473G>A | intron_variant | 2 | NM_001144072.2 | ENSP00000383911.3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250964Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135620
GnomAD4 exome AF: 0.000115 AC: 168AN: 1461868Hom.: 0 Cov.: 33 AF XY: 0.000124 AC XY: 90AN XY: 727236
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2024 | The c.776C>T (p.T259M) alteration is located in exon 3 (coding exon 1) of the GPR18 gene. This alteration results from a C to T substitution at nucleotide position 776, causing the threonine (T) at amino acid position 259 to be replaced by a methionine (M). 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