Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_170665.4(ATP2A2):c.81A>G(p.Glu27Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00961 in 1,579,124 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0095 ( 76 hom. )

Consequence

ATP2A2
NM_170665.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.564

Publications

4 publications found

Variant links:

Genes affected

ATP2A2 (HGNC:812): (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2) This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of the skeletal muscle. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol into the sarcoplasmic reticulum lumen, and is involved in regulation of the contraction/relaxation cycle. Mutations in this gene cause Darier-White disease, also known as keratosis follicularis, an autosomal dominant skin disorder characterized by loss of adhesion between epidermal cells and abnormal keratinization. Other types of mutations in this gene have been associated with various forms of muscular dystrophies. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2019]

ATP2A2 Gene-Disease associations (from GenCC):

acrokeratosis verruciformis
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P
Darier disease
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, PanelApp Australia, Illumina

ATP2A2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 12-110281870-A-G is Benign according to our data. Variant chr12-110281870-A-G is described in ClinVar as Benign. ClinVar VariationId is 307159.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.564 with no splicing effect.

BS2

High AC in GnomAd4 at 1555 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_170665.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ATP2A2	NM_170665.4	MANE Select	c.81A>G	p.Glu27Glu	synonymous	Exon 1 of 20	NP_733765.1
ATP2A2	NM_001413013.1		c.81A>G	p.Glu27Glu	synonymous	Exon 1 of 19	NP_001399942.1
ATP2A2	NM_001413014.1		c.81A>G	p.Glu27Glu	synonymous	Exon 1 of 22	NP_001399943.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ATP2A2	ENST00000539276.7	TSL:1 MANE Select	c.81A>G	p.Glu27Glu	synonymous	Exon 1 of 20	ENSP00000440045.2
ATP2A2	ENST00000308664.10	TSL:1	c.81A>G	p.Glu27Glu	synonymous	Exon 1 of 21	ENSP00000311186.6
ATP2A2	ENST00000377685.9	TSL:5	n.81A>G		non_coding_transcript_exon	Exon 1 of 20	ENSP00000366913.4

Frequencies

GnomAD3 genomes

AF:

0.0102

AC:

1554

AN:

151920

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00852

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00436

Gnomad FIN

AF:

0.0170

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00946

Gnomad OTH

AF:

0.00719

GnomAD2 exomes

AF:

0.00810

AC:

1638

AN:

202198

AF XY:

0.00784

show subpopulations

Gnomad AFR exome

AF:

0.0137

Gnomad AMR exome

AF:

0.00560

Gnomad ASJ exome

AF:

0.00183

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0184

Gnomad NFE exome

AF:

0.00908

Gnomad OTH exome

AF:

0.00969

GnomAD4 exome

AF:

0.00955

AC:

13627

AN:

1427096

Hom.:

Cov.:

AF XY:

0.00941

AC XY:

6658

AN XY:

707474

show subpopulations

African (AFR)

AF:

0.0139

AC:

428

AN:

30888

American (AMR)

AF:

0.00590

AC:

238

AN:

40324

Ashkenazi Jewish (ASJ)

AF:

0.00140

AC:

AN:

24966

East Asian (EAS)

AF:

0.00

AC:

AN:

37222

South Asian (SAS)

AF:

0.00547

AC:

443

AN:

80976

European-Finnish (FIN)

AF:

0.0180

AC:

927

AN:

51462

Middle Eastern (MID)

AF:

0.00282

AC:

AN:

5668

European-Non Finnish (NFE)

AF:

0.0101

AC:

11116

AN:

1096596

Other (OTH)

AF:

0.00719

AC:

424

AN:

58994

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

631

1262

1893

2524

3155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

434

868

1302

1736

2170

<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:

0.0102

AC:

1555

AN:

152028

Hom.:

Cov.:

AF XY:

0.0100

AC XY:

746

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.0136

AC:

563

AN:

41494

American (AMR)

AF:

0.00837

AC:

128

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.00144

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5130

South Asian (SAS)

AF:

0.00437

AC:

AN:

4810

European-Finnish (FIN)

AF:

0.0170

AC:

180

AN:

10586

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00946

AC:

643

AN:

67944

Other (OTH)

AF:

0.00712

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

153

229

306

382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00958

Hom.:

Bravo

AF:

0.00994

Asia WGS

AF:

0.00202

AC:

AN:

3470

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Keratosis follicularis (2)

Acrokeratosis verruciformis of Hopf (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.56

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Mutation Taster

=99/1

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs3026434

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over