X-151397011-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PVS1PM2BP6
The NM_001363810.1(VMA21):c.172G>T(p.Glu58*) variant causes a stop gained 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. Variant has been reported in ClinVar as Likely benign (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001363810.1 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VMA21 | NM_001363810.1 | c.172G>T | p.Glu58* | stop_gained | Exon 1 of 3 | NP_001350739.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000370361.5 | c.172G>T | p.Glu58* | stop_gained | Exon 2 of 4 | 5 | ENSP00000359386.1 | |||
ENSG00000287918 | ENST00000660681.2 | n.127C>A | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||||
ENSG00000287918 | ENST00000664935.1 | n.8C>A | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
VMA21-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.