Genetic Variant ATP12A:c.1882-95C>T (chr13-24701840-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001676.7(ATP12A):c.1882-95C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 1,517,908 control chromosomes in the GnomAD database, including 560 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 0.035 ( 162 hom., cov: 33)

Exomes 𝑓: 0.019 ( 398 hom. )

Consequence

ATP12A
NM_001676.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264

Publications

4 publications found

Variant links:

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]

ATP12A links:

ENSG00000285806 (HGNC:):

ENSG00000285806 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP12A	NM_001676.7 link	c.1882-95C>T		intron_variant	Intron 13 of 22	ENST00000381946.5	NP_001667.4
ATP12A	NM_001185085.2 link	c.1900-95C>T		intron_variant	Intron 13 of 22		NP_001172014.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ATP12A	ENST00000381946.5 link	c.1882-95C>T	intron_variant	Intron 13 of 22	1	NM_001676.7	ENSP00000371372.3
ATP12A	ENST00000218548.10 link	c.1900-95C>T	intron_variant	Intron 13 of 22	1		ENSP00000218548.6
ENSG00000285806	ENST00000782956.1 link	n.176-7081G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0347

AC:

5279

AN:

152204

Hom.:

160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0829

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0202

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.0508

Gnomad SAS

AF:

0.0298

Gnomad FIN

AF:

0.00668

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0144

Gnomad OTH

AF:

0.0301

GnomAD4 exome

AF:

0.0187

AC:

25475

AN:

1365586

Hom.:

398

AF XY:

0.0190

AC XY:

12907

AN XY:

679190

show subpopulations

African (AFR)

AF:

0.0839

AC:

2639

AN:

31464

American (AMR)

AF:

0.0118

AC:

511

AN:

43144

Ashkenazi Jewish (ASJ)

AF:

0.000579

AC:

AN:

24196

East Asian (EAS)

AF:

0.0694

AC:

2705

AN:

38988

South Asian (SAS)

AF:

0.0279

AC:

2253

AN:

80662

European-Finnish (FIN)

AF:

0.00862

AC:

412

AN:

47818

Middle Eastern (MID)

AF:

0.0134

AC:

AN:

4920

European-Non Finnish (NFE)

AF:

0.0151

AC:

15654

AN:

1037414

Other (OTH)

AF:

0.0214

AC:

1221

AN:

56980

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1209

2417

3626

4834

6043

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

672

1344

2016

2688

3360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0347

AC:

5285

AN:

152322

Hom.:

162

Cov.:

AF XY:

0.0336

AC XY:

2505

AN XY:

74500

show subpopulations

African (AFR)

AF:

0.0829

AC:

3447

AN:

41566

American (AMR)

AF:

0.0202

AC:

309

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.000577

AC:

AN:

3466

East Asian (EAS)

AF:

0.0505

AC:

262

AN:

5184

South Asian (SAS)

AF:

0.0294

AC:

142

AN:

4822

European-Finnish (FIN)

AF:

0.00668

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0144

AC:

981

AN:

68034

Other (OTH)

AF:

0.0298

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

248

495

743

990

1238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0210

Hom.:

Bravo

AF:

0.0382

Asia WGS

AF:

0.0400

AC:

137

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

5.1

(source)

DANN

Benign

0.60

PhyloP100

0.26

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over