Genetic Variant ATP10A:c.*1001A>G (chr15-25678340-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 ENST00000356865.11(ATP10A):c.*1001A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,782 control chromosomes in the GnomAD database, including 19,507 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 0.50 ( 19495 hom., cov: 31)

Exomes 𝑓: 0.55 ( 12 hom. )

Consequence

ATP10A
ENST00000356865.11 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.495

Publications

4 publications found

Variant links:

Genes affected

ATP10A (HGNC:13542): (ATPase phospholipid transporting 10A (putative)) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. This gene is maternally expressed. It maps within the most common interval of deletion responsible for Angelman syndrome, also known as 'happy puppet syndrome'. [provided by RefSeq, Jul 2008]

ATP10A 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10A	XM_011521828.3 link	c.4242+1259A>G		intron_variant	Intron 21 of 21		XP_011520130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000356865.11 link	c.*1001A>G		3_prime_UTR_variant	Exon 22 of 22	1		ENSP00000349325.6		O60312-1

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76106

AN:

151598

Hom.:

19465

Cov.:

show subpopulations

Gnomad AFR

AF:

0.596

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.491

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.465

GnomAD4 exome

AF:

0.547

AC:

AN:

Hom.:

Cov.:

AF XY:

0.620

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.833

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.545

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.534

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.502

AC:

76188

AN:

151718

Hom.:

19495

Cov.:

AF XY:

0.501

AC XY:

37087

AN XY:

74092

show subpopulations

African (AFR)

AF:

0.597

AC:

24674

AN:

41362

American (AMR)

AF:

0.491

AC:

7494

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.437

AC:

1516

AN:

3466

East Asian (EAS)

AF:

0.379

AC:

1943

AN:

5126

South Asian (SAS)

AF:

0.441

AC:

2106

AN:

4778

European-Finnish (FIN)

AF:

0.492

AC:

5161

AN:

10496

Middle Eastern (MID)

AF:

0.476

AC:

140

AN:

294

European-Non Finnish (NFE)

AF:

0.467

AC:

31690

AN:

67916

Other (OTH)

AF:

0.465

AC:

981

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1914

3828

5742

7656

9570

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<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:

0.474

Hom.:

29150

Bravo

AF:

0.503

Asia WGS

AF:

0.415

AC:

1445

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.6

(source)

DANN

Benign

0.38

PhyloP100

-0.49

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