Variant X-40606021-A-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 NM_005765.3(ATP6AP2):c.*266A>T variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.08 in 311,272 control chromosomes in the GnomAD database, including 2,994 homozygotes. There are 6,480 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 2070 hom., 4297 hem., cov: 23)

Exomes 𝑓: 0.048 ( 924 hom. 2183 hem. )

Consequence

ATP6AP2
NM_005765.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.97

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:

ATP6AP2 (HGNC:):

ATP6AP2 links:

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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 (BayesDel_noAF=-0.78).

BP6

Variant X-40606021-A-T is Benign according to our data. Variant chrX-40606021-A-T is described in ClinVar as [Benign]. Clinvar id is 1267961.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6AP2	NM_005765.3 linkuse as main transcript	c.*266A>T		3_prime_UTR_variant	9/9	ENST00000636580.2	NP_005756.2	O75787-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6AP2	ENST00000636580.2 linkuse as main transcript	c.*266A>T		3_prime_UTR_variant	9/9	1	NM_005765.3	ENSP00000490083.1		O75787-1

Frequencies

GnomAD3 genomes

AF:

0.138

AC:

15372

AN:

111296

Hom.:

2070

Cov.:

AF XY:

0.128

AC XY:

4275

AN XY:

33518

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.193

Gnomad ASJ

AF:

0.0174

Gnomad EAS

AF:

0.158

Gnomad SAS

AF:

0.0166

Gnomad FIN

AF:

0.00414

Gnomad MID

AF:

0.0460

Gnomad NFE

AF:

0.00576

Gnomad OTH

AF:

0.132

GnomAD4 exome

AF:

0.0475

AC:

9503

AN:

199924

Hom.:

924

Cov.:

AF XY:

0.0444

AC XY:

2183

AN XY:

49130

show subpopulations

Gnomad4 AFR exome

AF:

0.411

Gnomad4 AMR exome

AF:

0.241

Gnomad4 ASJ exome

AF:

0.0194

Gnomad4 EAS exome

AF:

0.219

Gnomad4 SAS exome

AF:

0.0170

Gnomad4 FIN exome

AF:

0.00525

Gnomad4 NFE exome

AF:

0.00515

Gnomad4 OTH exome

AF:

0.0650

GnomAD4 genome

AF:

0.138

AC:

15393

AN:

111348

Hom.:

2070

Cov.:

AF XY:

0.128

AC XY:

4297

AN XY:

33580

show subpopulations

Gnomad4 AFR

AF:

0.401

Gnomad4 AMR

AF:

0.193

Gnomad4 ASJ

AF:

0.0174

Gnomad4 EAS

AF:

0.158

Gnomad4 SAS

AF:

0.0159

Gnomad4 FIN

AF:

0.00414

Gnomad4 NFE

AF:

0.00576

Gnomad4 OTH

AF:

0.130

Alfa

AF:

0.0828

Hom.:

476

Bravo

AF:

0.173

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	Jun 18, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

DANN

Benign

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

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