X-151397088-G-T

Variant summary

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

The NM_001363810.1(VMA21):​c.218+31G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 13647 hom., 18281 hem., cov: 22)
Exomes 𝑓: 0.52 ( 30628 hom. 56665 hem. )
Failed GnomAD Quality Control

Consequence

VMA21
NM_001363810.1 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -2.68
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant X-151397088-G-T is Benign according to our data. Variant chrX-151397088-G-T is described in ClinVar as [Benign]. Clinvar id is 1283501.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
VMA21NM_001363810.1 linkc.218+31G>T intron_variant Intron 1 of 2 NP_001350739.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VMA21ENST00000370361.5 linkc.218+31G>T intron_variant Intron 2 of 3 5 ENSP00000359386.1 Q3ZAQ7-2
ENSG00000287918ENST00000660681.2 linkn.50C>A non_coding_transcript_exon_variant Exon 1 of 2
ENSG00000287918ENST00000668689.1 linkn.55C>A non_coding_transcript_exon_variant Exon 1 of 2
VMA21ENST00000477649.1 linkn.133+441G>T intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.574
AC:
62881
AN:
109605
Hom.:
13638
Cov.:
22
AF XY:
0.561
AC XY:
18259
AN XY:
32571
show subpopulations
Gnomad AFR
AF:
0.753
Gnomad AMI
AF:
0.495
Gnomad AMR
AF:
0.382
Gnomad ASJ
AF:
0.500
Gnomad EAS
AF:
0.181
Gnomad SAS
AF:
0.417
Gnomad FIN
AF:
0.559
Gnomad MID
AF:
0.483
Gnomad NFE
AF:
0.549
Gnomad OTH
AF:
0.530
GnomAD3 exomes
AF:
0.484
AC:
18580
AN:
38363
Hom.:
4253
AF XY:
0.547
AC XY:
2588
AN XY:
4733
show subpopulations
Gnomad AFR exome
AF:
0.776
Gnomad AMR exome
AF:
0.334
Gnomad ASJ exome
AF:
0.521
Gnomad EAS exome
AF:
0.186
Gnomad SAS exome
AF:
0.468
Gnomad FIN exome
AF:
0.581
Gnomad NFE exome
AF:
0.577
Gnomad OTH exome
AF:
0.499
GnomAD4 exome
AF:
0.517
AC:
170712
AN:
330499
Hom.:
30628
Cov.:
4
AF XY:
0.537
AC XY:
56665
AN XY:
105563
show subpopulations
Gnomad4 AFR exome
AF:
0.771
Gnomad4 AMR exome
AF:
0.331
Gnomad4 ASJ exome
AF:
0.506
Gnomad4 EAS exome
AF:
0.199
Gnomad4 SAS exome
AF:
0.470
Gnomad4 FIN exome
AF:
0.560
Gnomad4 NFE exome
AF:
0.555
Gnomad4 OTH exome
AF:
0.519
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.574
AC:
62909
AN:
109638
Hom.:
13647
Cov.:
22
AF XY:
0.561
AC XY:
18281
AN XY:
32614
show subpopulations
Gnomad4 AFR
AF:
0.753
Gnomad4 AMR
AF:
0.381
Gnomad4 ASJ
AF:
0.500
Gnomad4 EAS
AF:
0.182
Gnomad4 SAS
AF:
0.416
Gnomad4 FIN
AF:
0.559
Gnomad4 NFE
AF:
0.549
Gnomad4 OTH
AF:
0.532
Alfa
AF:
0.437
Hom.:
3490
Bravo
AF:
0.562

ClinVar

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

Submissions by phenotype

not provided Benign:2
May 15, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.035
DANN
Benign
0.31

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: rs176452; hg19: chrX-150565560; API