rs12020712

Positions:

• chr13-113653810-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000705.4(ATP4B):​c.242-376G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,234 control chromosomes in the GnomAD database, including 3,321 homozygotes. 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 0.20 (3321 hom., cov: 34)
• Consequence: ATP4B NM_000705.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

ATP4B (HGNC:820): (ATPase H+/K+ transporting subunit beta) The protein encoded by this gene belongs to a family of P-type cation-transporting ATPases. The gastric H+, K+-ATPase is a heterodimer consisting of a high molecular weight catalytic alpha subunit and a smaller but heavily glycosylated beta subunit. This enzyme is a proton pump that catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. It is also responsible for gastric acid secretion. This gene encodes the beta subunit of the gastric H+, K+-ATPase. [provided by RefSeq, Jul 2008]

GRK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP4B	NM_000705.4	c.242-376G>A		intron_variant		ENST00000335288.5
GRK1	XM_047430493.1	c.-7+5566C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP4B	ENST00000335288.5	c.242-376G>A		intron_variant		1	NM_000705.4	P1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31090 AN: 152116 Hom.: 3319 Cov.: 34

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.204 AC: 31109 AN: 152234 Hom.: 3321 Cov.: 34 AF XY: 0.201 AC XY: 14944 AN XY: 74432

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.211

Alfa AF: 0.208 Hom.: 3333

Bravo AF: 0.212

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs12020712; hg19: chr13-114308125;