Variant X-154428737-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001183.6(ATP6AP1):c.45G>A(p.Arg15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,146,269 control chromosomes in the GnomAD database, including 5,214 homozygotes. There are 42,749 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 473 hom., 3776 hem., cov: 25)

Exomes 𝑓: 0.11 ( 4741 hom. 38973 hem. )

Consequence

ATP6AP1
NM_001183.6 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.519

Variant links:

Genes affected

ATP6AP1 (HGNC:868): (ATPase H+ transporting accessory protein 1) This gene encodes a component of a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Vacuolar ATPase (V-ATPase) is comprised of a cytosolic V1 (site of the ATP catalytic site) and a transmembrane V0 domain. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, and receptor-mediated endocytosis. The encoded protein of this gene may assist in the V-ATPase-mediated acidification of neuroendocrine secretory granules. This protein may also play a role in early development. [provided by RefSeq, Aug 2013]

ATP6AP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant X-154428737-G-A is Benign according to our data. Variant chrX-154428737-G-A is described in ClinVar as [Benign]. Clinvar id is 770830.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.519 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6AP1	NM_001183.6 linkuse as main transcript	c.45G>A	p.Arg15=	synonymous_variant	1/10	ENST00000369762.7	NP_001174.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6AP1	ENST00000369762.7 linkuse as main transcript	c.45G>A	p.Arg15=	synonymous_variant	1/10	1	NM_001183.6	ENSP00000358777	P1

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

11909

AN:

113143

Hom.:

465

Cov.:

AF XY:

0.107

AC XY:

3768

AN XY:

35297

show subpopulations

Gnomad AFR

AF:

0.0915

Gnomad AMI

AF:

0.00875

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.0600

Gnomad EAS

AF:

0.0617

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.0464

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.0930

GnomAD4 exome

AF:

0.115

AC:

118410

AN:

1033077

Hom.:

4741

Cov.:

AF XY:

0.116

AC XY:

38973

AN XY:

335163

show subpopulations

Gnomad4 AFR exome

AF:

0.0854

Gnomad4 AMR exome

AF:

0.141

Gnomad4 ASJ exome

AF:

0.0637

Gnomad4 EAS exome

AF:

0.0744

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.148

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.105

AC:

11928

AN:

113192

Hom.:

473

Cov.:

AF XY:

0.107

AC XY:

3776

AN XY:

35356

show subpopulations

Gnomad4 AFR

AF:

0.0914

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.0600

Gnomad4 EAS

AF:

0.0608

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.140

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.111

Hom.:

982

Bravo

AF:

0.103

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

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

8.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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