dbSNP rs735770: ATP12A:c.547-107T>C (chr13-24690231-T-C) – 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.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
NM_001676.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.31

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:

Genome browser will be placed here

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 (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP12A	NM_001676.7 link	c.547-107T>C		intron_variant	Intron 5 of 22	ENST00000381946.5	NP_001667.4
ATP12A	NM_001185085.2 link	c.547-107T>C		intron_variant	Intron 5 of 22		NP_001172014.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ATP12A	ENST00000381946.5 link	c.547-107T>C	intron_variant	Intron 5 of 22	1	NM_001676.7	ENSP00000371372.3
ATP12A	ENST00000218548.10 link	c.547-107T>C	intron_variant	Intron 5 of 22	1		ENSP00000218548.6
ENSG00000285806	ENST00000782956.1 link	n.281-1143A>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35609

AN:

151704

Hom.:

4631

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.167

AC:

5135

AN:

30702

American (AMR)

AF:

0.457

AC:

16465

AN:

35992

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

3844

AN:

21206

East Asian (EAS)

AF:

0.505

AC:

19725

AN:

39036

South Asian (SAS)

AF:

0.316

AC:

23317

AN:

73880

European-Finnish (FIN)

AF:

0.207

AC:

9041

AN:

43682

Middle Eastern (MID)

AF:

0.203

AC:

780

AN:

3838

European-Non Finnish (NFE)

AF:

0.224

AC:

236355

AN:

1055380

Other (OTH)

AF:

0.243

AC:

13668

AN:

56262

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

12157

24314

36470

48627

60784

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8552

17104

25656

34208

42760

<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:

0.235

AC:

35643

AN:

151822

Hom.:

4638

Cov.:

AF XY:

0.241

AC XY:

17887

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.173

AC:

7148

AN:

41376

American (AMR)

AF:

0.382

AC:

5831

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.186

AC:

643

AN:

3460

East Asian (EAS)

AF:

0.475

AC:

2450

AN:

5158

South Asian (SAS)

AF:

0.317

AC:

1521

AN:

4802

European-Finnish (FIN)

AF:

0.219

AC:

2306

AN:

10552

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.222

AC:

15087

AN:

67924

Other (OTH)

AF:

0.212

AC:

446

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1346

2692

4039

5385

6731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.229

Hom.:

553

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

(source)

DANN

Benign

0.40

PhyloP100

-2.3

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