13-24690231-T-C

Position:

• chr13-24690231-T-C

Variant summary

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

The ENST00000381946.5(ATP12A):​c.547-107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 1,511,800 control chromosomes in the GnomAD database, including 47,807 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 0.23 (4638 hom., cov: 31)
  • Exomes 𝑓: 0.24 (43169 hom.)
• Consequence: ATP12A ENST00000381946.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

Genes affected

ATP12A (HGNC:13816): (ATPase H+/K+ transporting non-gastric alpha2 subunit) The protein encoded by this gene belongs to the family of P-type cation transport ATPases. This gene encodes a catalytic subunit of the ouabain-sensitive H+/K+ -ATPase that catalyzes the hydrolysis of ATP coupled with the exchange of H(+) and K(+) ions across the plasma membrane. It is also responsible for potassium absorption in various tissues. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP12A	NM_001676.7	c.547-107T>C		intron_variant		ENST00000381946.5	NP_001667.4
ATP12A	NM_001185085.2	c.547-107T>C		intron_variant			NP_001172014.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP12A	ENST00000381946.5	c.547-107T>C		intron_variant		1	NM_001676.7	ENSP00000371372	A1
ATP12A	ENST00000218548.10	c.547-107T>C		intron_variant		1		ENSP00000218548	P4

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35609 AN: 151704 Hom.: 4631 Cov.: 31

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.211

GnomAD4 exome AF: 0.241 AC: 328330 AN: 1359978 Hom.: 43169 AF XY: 0.243 AC XY: 162842 AN XY: 671270

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.457

Gnomad4 ASJ exome AF: 0.181

Gnomad4 EAS exome AF: 0.505

Gnomad4 SAS exome AF: 0.316

Gnomad4 FIN exome AF: 0.207

Gnomad4 NFE exome AF: 0.224

Gnomad4 OTH exome AF: 0.243

GnomAD4 genome AF: 0.235 AC: 35643 AN: 151822 Hom.: 4638 Cov.: 31 AF XY: 0.241 AC XY: 17887 AN XY: 74158

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.212

Alfa AF: 0.231 Hom.: 538

Bravo AF: 0.244

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs735770; hg19: chr13-25264369; COSMIC: COSV54516754;