rs140025330
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000330374.7(VMA21):c.166G>A(p.Ala56Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000448 in 1,204,401 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
ENST00000330374.7 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VMA21 | NM_001017980.4 | c.166G>A | p.Ala56Thr | missense_variant, splice_region_variant | 3/3 | ENST00000330374.7 | NP_001017980.1 | |
VMA21 | NM_001363810.1 | c.331G>A | p.Ala111Thr | missense_variant, splice_region_variant | 3/3 | NP_001350739.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VMA21 | ENST00000330374.7 | c.166G>A | p.Ala56Thr | missense_variant, splice_region_variant | 3/3 | 1 | NM_001017980.4 | ENSP00000333255 | P1 | |
VMA21 | ENST00000370361.5 | c.331G>A | p.Ala111Thr | missense_variant, splice_region_variant | 4/4 | 5 | ENSP00000359386 | |||
VMA21 | ENST00000477649.1 | n.246G>A | splice_region_variant, non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 22AN: 107839Hom.: 0 Cov.: 22 AF XY: 0.000131 AC XY: 4AN XY: 30561
GnomAD3 exomes AF: 0.0000716 AC: 13AN: 181559Hom.: 0 AF XY: 0.0000302 AC XY: 2AN XY: 66229
GnomAD4 exome AF: 0.0000292 AC: 32AN: 1096562Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 7AN XY: 362168
GnomAD4 genome AF: 0.000204 AC: 22AN: 107839Hom.: 0 Cov.: 22 AF XY: 0.000131 AC XY: 4AN XY: 30561
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.166G>A (p.A56T) alteration is located in exon 3 (coding exon 3) of the VMA21 gene. This alteration results from a G to A substitution at nucleotide position 166, causing the alanine (A) at amino acid position 56 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
X-linked myopathy with excessive autophagy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 56 of the VMA21 protein (p.Ala56Thr). This variant is present in population databases (rs140025330, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with VMA21-related conditions. ClinVar contains an entry for this variant (Variation ID: 570316). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at