chrX-9725772-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000273.3(GPR143):c.1189G>A(p.Ala397Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_000273.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR143 | NM_000273.3 | c.1189G>A | p.Ala397Thr | missense_variant | Exon 9 of 9 | ENST00000467482.6 | NP_000264.2 | |
GPR143 | XM_024452388.2 | c.937G>A | p.Ala313Thr | missense_variant | Exon 9 of 9 | XP_024308156.1 | ||
GPR143 | XM_005274541.4 | c.*164G>A | 3_prime_UTR_variant | Exon 9 of 9 | XP_005274598.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR143 | ENST00000467482.6 | c.1189G>A | p.Ala397Thr | missense_variant | Exon 9 of 9 | 1 | NM_000273.3 | ENSP00000417161.1 | ||
TBL1X | ENST00000647060.1 | c.1554+10769C>T | intron_variant | Intron 15 of 15 | ENSP00000495467.1 |
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 21
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at