X-151396927-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001363810.1(VMA21):c.88C>T(p.Arg30Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000383 in 522,144 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001363810.1 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 |
---|---|---|---|---|---|---|---|---|
VMA21 | NM_001363810.1 | c.88C>T | p.Arg30Cys | missense_variant | Exon 1 of 3 | NP_001350739.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000370361.5 | c.88C>T | p.Arg30Cys | missense_variant | Exon 2 of 4 | 5 | ENSP00000359386.1 | |||
ENSG00000287918 | ENST00000660681.2 | n.211G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | ||||||
ENSG00000287918 | ENST00000664935.1 | n.92G>A | non_coding_transcript_exon_variant | Exon 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00000904 AC: 1AN: 110570Hom.: 0 Cov.: 21 AF XY: 0.0000305 AC XY: 1AN XY: 32834
GnomAD4 exome AF: 0.00000243 AC: 1AN: 411574Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 151736
GnomAD4 genome AF: 0.00000904 AC: 1AN: 110570Hom.: 0 Cov.: 21 AF XY: 0.0000305 AC XY: 1AN XY: 32834
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: VMA21 c.-382C>T is located in the untranscribed region upstream of the VMA21 gene region. The variant was absent in 20650 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-382C>T in individuals affected with X-Linked Myopathy With Excessive Autophagy and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at