chr13-24690963-G-A

Variant names:

• chr13-24690963-G-A
• rs114726296
• NM_001676.7:c.800-19G>A

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001676.7(ATP12A):​c.800-19G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000517 in 1,612,872 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0027 (2 hom., cov: 32)
  • Exomes 𝑓: 0.00029 (3 hom.)
• Consequence: ATP12A NM_001676.7 intron
• Scores: Splicing: ADA: 0.9924
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.225
• Publications: 3 publications found

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]

ENSG00000285806 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 13-24690963-G-A is Benign according to our data. Variant chr13-24690963-G-A is described in ClinVar as [Benign]. Clinvar id is 784480.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP12A	NM_001676.7	c.800-19G>A		intron_variant	Intron 7 of 22	ENST00000381946.5	NP_001667.4
ATP12A	NM_001185085.2	c.800-1G>A		splice_acceptor_variant, intron_variant	Intron 7 of 22		NP_001172014.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP12A	ENST00000381946.5	c.800-19G>A		intron_variant	Intron 7 of 22	1	NM_001676.7	ENSP00000371372.3
ATP12A	ENST00000218548.10	c.800-1G>A		splice_acceptor_variant, intron_variant	Intron 7 of 22	1		ENSP00000218548.6
ENSG00000285806	ENST00000782956.1	n.281-1875C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.00270 AC: 410 AN: 152118 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00963

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.000957

GnomAD2 exomes AF: 0.000765 AC: 192 AN: 250942 AF XY: 0.000560

Gnomad AFR exome AF: 0.0113

Gnomad AMR exome AF: 0.000202

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000292 AC: 426 AN: 1460636 Hom.: 3 Cov.: 32 AF XY: 0.000273 AC XY: 198 AN XY: 726360

African (AFR) AF: 0.0113 AC: 378 AN: 33448

American (AMR) AF: 0.000291 AC: 13 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26130

East Asian (EAS) AF: 0.00 AC: 0 AN: 39672

South Asian (SAS) AF: 0.00 AC: 0 AN: 86244

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53408

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5758

European-Non Finnish (NFE) AF: 0.00000720 AC: 8 AN: 1110914

Other (OTH) AF: 0.000414 AC: 25 AN: 60352

GnomAD4 genome AF: 0.00268 AC: 408 AN: 152236 Hom.: 2 Cov.: 32 AF XY: 0.00251 AC XY: 187 AN XY: 74444

African (AFR) AF: 0.00955 AC: 397 AN: 41556

American (AMR) AF: 0.000327 AC: 5 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4812

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 68000

Other (OTH) AF: 0.000947 AC: 2 AN: 2112

Alfa AF: 0.000130 Hom.: 0

ExAC AF: 0.000931 AC: 113

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.77	T
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.64
Eigen	Benign	-0.11
Eigen_PC	Benign	-0.50
FATHMM_MKL	Benign	0.0036	N
PhyloP100		-0.23
GERP RS		-2.0
Mutation Taster		=96/4	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
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

Other links and lift over

dbSNP: rs114726296; hg19: chr13-25265101;