Variant chrX-151397088-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000668689.1(ENSG00000287918):n.55C>A variant causes a non coding transcript exon 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

ENST00000668689.1 non_coding_transcript_exon

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.68

Variant links:

Genes affected

(HGNC:):

links:

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

VMA21 links:

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/exons	MANE	UniProt
VMA21	NM_001363810.1 linkuse as main transcript	c.218+31G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	UniProt
	ENST00000668689.1 linkuse as main transcript	n.55C>A	non_coding_transcript_exon_variant	1/2
VMA21	ENST00000370361.5 linkuse as main transcript	c.218+31G>T	intron_variant		5	Q3ZAQ7-2
	ENST00000660681.2 linkuse as main transcript	n.50C>A	non_coding_transcript_exon_variant	1/2
VMA21	ENST00000477649.1 linkuse as main transcript	n.133+441G>T	intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

62881

AN:

109605

Hom.:

13638

Cov.:

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.:

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.:

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over