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

Genomes: 𝑓 0.00020 ( 0 hom., 4 hem., cov: 22)
Exomes 𝑓: 0.000029 ( 0 hom. 7 hem. )

Consequence

VMA21
ENST00000330374.7 missense, splice_region

Scores

1
16

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 1.31
Variant links:
Genes affected
VMA21 (HGNC:22082): (vacuolar ATPase assembly factor VMA21) This gene encodes a chaperone for assembly of lysosomal vacuolar ATPase.[provided by RefSeq, Jul 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.029051095).
BS2
High Hemizygotes in GnomAd4 at 4 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
VMA21NM_001017980.4 linkuse as main transcriptc.166G>A p.Ala56Thr missense_variant, splice_region_variant 3/3 ENST00000330374.7 NP_001017980.1
VMA21NM_001363810.1 linkuse as main transcriptc.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
VMA21ENST00000330374.7 linkuse as main transcriptc.166G>A p.Ala56Thr missense_variant, splice_region_variant 3/31 NM_001017980.4 ENSP00000333255 P1Q3ZAQ7-1
VMA21ENST00000370361.5 linkuse as main transcriptc.331G>A p.Ala111Thr missense_variant, splice_region_variant 4/45 ENSP00000359386 Q3ZAQ7-2
VMA21ENST00000477649.1 linkuse as main transcriptn.246G>A splice_region_variant, non_coding_transcript_exon_variant 3/33

Frequencies

GnomAD3 genomes
AF:
0.000204
AC:
22
AN:
107839
Hom.:
0
Cov.:
22
AF XY:
0.000131
AC XY:
4
AN XY:
30561
show subpopulations
Gnomad AFR
AF:
0.000613
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000289
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000573
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000716
AC:
13
AN:
181559
Hom.:
0
AF XY:
0.0000302
AC XY:
2
AN XY:
66229
show subpopulations
Gnomad AFR exome
AF:
0.000914
Gnomad AMR exome
AF:
0.0000366
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000292
AC:
32
AN:
1096562
Hom.:
0
Cov.:
31
AF XY:
0.0000193
AC XY:
7
AN XY:
362168
show subpopulations
Gnomad4 AFR exome
AF:
0.000949
Gnomad4 AMR exome
AF:
0.0000569
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000357
Gnomad4 OTH exome
AF:
0.0000434
GnomAD4 genome
AF:
0.000204
AC:
22
AN:
107839
Hom.:
0
Cov.:
22
AF XY:
0.000131
AC XY:
4
AN XY:
30561
show subpopulations
Gnomad4 AFR
AF:
0.000613
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000289
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000573
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.000223
ESP6500AA
AF:
0.000782
AC:
3
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000741
AC:
9

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 30, 2024The 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2023This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.064
BayesDel_addAF
Benign
-0.56
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
15
DANN
Uncertain
0.98
DEOGEN2
Benign
0.0010
.;T
FATHMM_MKL
Benign
0.74
D
LIST_S2
Benign
0.82
T;T
M_CAP
Benign
0.025
D
MetaRNN
Benign
0.029
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.71
.;N
MutationTaster
Benign
0.91
N;N
PrimateAI
Benign
0.39
T
PROVEAN
Benign
0.11
N;N
REVEL
Benign
0.048
Sift
Benign
0.33
T;T
Sift4G
Benign
0.50
T;T
Polyphen
0.0
.;B
Vest4
0.16
MVP
0.37
MPC
0.75
ClinPred
0.029
T
GERP RS
2.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.075
gMVP
0.76

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs140025330; hg19: chrX-150573390; COSMIC: COSV57757052; API