rs2968915

Positions:

• chrX-40580182-G-A
• chrX-40580182-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000436783.6(ATP6AP2):​c.-111+435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.87 (29194 hom., 27988 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ATP6AP2 ENST00000436783.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

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]

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40580182G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6AP2	ENST00000436783.6	c.-111+435G>A		intron_variant		5		ENSP00000403969.2

Frequencies

GnomAD3 genomes AF: 0.866 AC: 95246 AN: 110037 Hom.: 29199 Cov.: 22 AF XY: 0.866 AC XY: 27946 AN XY: 32257

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.909

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.876

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: 0.865 AC: 95277 AN: 110092 Hom.: 29194 Cov.: 22 AF XY: 0.866 AC XY: 27988 AN XY: 32322

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.875

Alfa AF: 0.896 Hom.: 90863

Bravo AF: 0.866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.1
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2968915; hg19: chrX-40439434;