Variant chrX-40588704-T-TTTTG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_005765.3(ATP6AP2):c.38-274_38-271dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.93 ( 33922 hom., 27622 hem., cov: 0)

Failed GnomAD Quality Control

Consequence

ATP6AP2
NM_005765.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.631

Variant links:

Genes affected

ATP6AP2 (HGNC:18305): (ATPase H+ transporting accessory protein 2) This gene encodes a protein that is associated with adenosine triphosphatases (ATPases). Proton-translocating ATPases have fundamental roles in energy conservation, secondary active transport, acidification of intracellular compartments, and cellular pH homeostasis. There are three classes of ATPases- F, P, and V. The vacuolar (V-type) ATPases have a transmembrane proton-conducting sector and an extramembrane catalytic sector. The encoded protein has been found associated with the transmembrane sector of the V-type ATPases. [provided by RefSeq, Jul 2008]

ATP6AP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6

Variant X-40588704-T-TTTTG is Benign according to our data. Variant chrX-40588704-T-TTTTG is described in ClinVar as [Benign]. Clinvar id is 668777.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP6AP2	NM_005765.3 linkuse as main transcript	c.38-274_38-271dup		intron_variant		ENST00000636580.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP6AP2	ENST00000636580.2 linkuse as main transcript	c.38-274_38-271dup		intron_variant		1	NM_005765.3	P3	O75787-1

Frequencies

GnomAD3 genomes

AF:

0.932

AC:

100032

AN:

107320

Hom.:

33928

Cov.:

AF XY:

0.927

AC XY:

27555

AN XY:

29728

show subpopulations

Gnomad AFR

AF:

0.986

Gnomad AMI

AF:

0.951

Gnomad AMR

AF:

0.930

Gnomad ASJ

AF:

0.932

Gnomad EAS

AF:

0.830

Gnomad SAS

AF:

0.957

Gnomad FIN

AF:

0.872

Gnomad MID

AF:

0.966

Gnomad NFE

AF:

0.913

Gnomad OTH

AF:

0.940

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.932

AC:

100088

AN:

107373

Hom.:

33922

Cov.:

AF XY:

0.927

AC XY:

27622

AN XY:

29793

show subpopulations

Gnomad4 AFR

AF:

0.986

Gnomad4 AMR

AF:

0.930

Gnomad4 ASJ

AF:

0.932

Gnomad4 EAS

AF:

0.831

Gnomad4 SAS

AF:

0.957

Gnomad4 FIN

AF:

0.872

Gnomad4 NFE

AF:

0.913

Gnomad4 OTH

AF:

0.938

Alfa

AF:

0.911

Hom.:

7083

Asia WGS

AF:

0.904

AC:

2278

AN:

2519

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 14, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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