chrX-151396858-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001363810.1(VMA21):ā€‹c.19G>Cā€‹(p.Gly7Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 9/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.57 ( 13688 hom., 17503 hem., cov: 21)
Exomes š‘“: 0.50 ( 34664 hom. 75315 hem. )
Failed GnomAD Quality Control

Consequence

VMA21
NM_001363810.1 missense

Scores

1
10

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.736
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=1.4144747E-5).
BP6
Variant X-151396858-G-C is Benign according to our data. Variant chrX-151396858-G-C is described in ClinVar as [Benign]. Clinvar id is 1684210.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VMA21NM_001363810.1 linkc.19G>C p.Gly7Arg missense_variant Exon 1 of 3 NP_001350739.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VMA21ENST00000370361.5 linkc.19G>C p.Gly7Arg missense_variant Exon 2 of 4 5 ENSP00000359386.1 Q3ZAQ7-2
ENSG00000287918ENST00000660681.2 linkn.280C>G non_coding_transcript_exon_variant Exon 1 of 2
ENSG00000287918ENST00000664935.1 linkn.161C>G non_coding_transcript_exon_variant Exon 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.570
AC:
62315
AN:
109233
Hom.:
13679
Cov.:
21
AF XY:
0.552
AC XY:
17468
AN XY:
31621
show subpopulations
Gnomad AFR
AF:
0.753
Gnomad AMI
AF:
0.492
Gnomad AMR
AF:
0.380
Gnomad ASJ
AF:
0.496
Gnomad EAS
AF:
0.172
Gnomad SAS
AF:
0.409
Gnomad FIN
AF:
0.544
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.547
Gnomad OTH
AF:
0.526
GnomAD3 exomes
AF:
0.461
AC:
46235
AN:
100226
Hom.:
7620
AF XY:
0.460
AC XY:
16402
AN XY:
35662
show subpopulations
Gnomad AFR exome
AF:
0.764
Gnomad AMR exome
AF:
0.309
Gnomad ASJ exome
AF:
0.489
Gnomad EAS exome
AF:
0.173
Gnomad SAS exome
AF:
0.436
Gnomad FIN exome
AF:
0.542
Gnomad NFE exome
AF:
0.541
Gnomad OTH exome
AF:
0.469
GnomAD4 exome
AF:
0.502
AC:
205927
AN:
409878
Hom.:
34664
Cov.:
0
AF XY:
0.500
AC XY:
75315
AN XY:
150492
show subpopulations
Gnomad4 AFR exome
AF:
0.762
Gnomad4 AMR exome
AF:
0.319
Gnomad4 ASJ exome
AF:
0.490
Gnomad4 EAS exome
AF:
0.192
Gnomad4 SAS exome
AF:
0.439
Gnomad4 FIN exome
AF:
0.553
Gnomad4 NFE exome
AF:
0.544
Gnomad4 OTH exome
AF:
0.510
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.571
AC:
62355
AN:
109278
Hom.:
13688
Cov.:
21
AF XY:
0.553
AC XY:
17503
AN XY:
31676
show subpopulations
Gnomad4 AFR
AF:
0.753
Gnomad4 AMR
AF:
0.380
Gnomad4 ASJ
AF:
0.496
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.409
Gnomad4 FIN
AF:
0.544
Gnomad4 NFE
AF:
0.547
Gnomad4 OTH
AF:
0.528
Alfa
AF:
0.432
Hom.:
3356
Bravo
AF:
0.561
TwinsUK
AF:
0.538
AC:
1994
ALSPAC
AF:
0.541
AC:
1564
ExAC
AF:
0.456
AC:
7873

ClinVar

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

Submissions by phenotype

X-linked myopathy with excessive autophagy Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabDec 05, 2021- -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.94
T
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.54
DANN
Benign
0.66
FATHMM_MKL
Benign
0.065
N
LIST_S2
Benign
0.28
T
MetaRNN
Benign
0.000014
T
MetaSVM
Benign
-0.94
T
PROVEAN
Benign
0.18
N
REVEL
Benign
0.049
Sift
Pathogenic
0.0
D
Vest4
0.032
ClinPred
0.0059
T
GERP RS
-2.6
gMVP
0.053

Splicing

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: rs176451; hg19: chrX-150565330; COSMIC: COSV57756648; COSMIC: COSV57756648; API