dbSNP rs2066707: ATP10A:c.*695C>G (chr15-25678646-G-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.*695C>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 0.633 in 152,066 control chromosomes in the GnomAD database, including 30,940 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 0.63 ( 30938 hom., cov: 33)

Exomes 𝑓: 0.63 ( 2 hom. )

Consequence

ATP10A
ENST00000356865.11 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.820

Publications

8 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10A	NM_024490.4 link	c.*695C>G		downstream_gene_variant		ENST00000555815.7	NP_077816.1	O60312-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ATP10A	ENST00000356865.11 link	c.*695C>G	3_prime_UTR_variant	Exon 22 of 22	1		ENSP00000349325.6	O60312-1
ATP10A	ENST00000555815.7 link	c.*695C>G	downstream_gene_variant		5	NM_024490.4	ENSP00000450480.2	O60312-1
ATP10A	ENST00000673805.1 link	n.*90C>G	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.632

AC:

96095

AN:

151940

Hom.:

30892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.731

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.625

Gnomad ASJ

AF:

0.608

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.611

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.605

Gnomad OTH

AF:

0.629

GnomAD4 exome

AF:

0.625

AC:

AN:

Hom.:

Cov.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

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:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.633

AC:

96197

AN:

152058

Hom.:

30938

Cov.:

AF XY:

0.628

AC XY:

46672

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.731

AC:

30330

AN:

41484

American (AMR)

AF:

0.625

AC:

9554

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.608

AC:

2106

AN:

3466

East Asian (EAS)

AF:

0.380

AC:

1960

AN:

5158

South Asian (SAS)

AF:

0.536

AC:

2581

AN:

4816

European-Finnish (FIN)

AF:

0.611

AC:

6448

AN:

10546

Middle Eastern (MID)

AF:

0.622

AC:

183

AN:

294

European-Non Finnish (NFE)

AF:

0.605

AC:

41098

AN:

67976

Other (OTH)

AF:

0.626

AC:

1323

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1779

3558

5338

7117

8896

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<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:

0.624

Hom.:

3684

Bravo

AF:

0.635

Asia WGS

AF:

0.464

AC:

1615

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.60

(source)

DANN

Benign

0.43

PhyloP100

-0.82

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over