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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000356865.11, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000356865.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10A	NM_024490.4	MANE Select	c.*695C>G		downstream_gene	N/A	NP_077816.1	O60312-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ATP10A	ENST00000356865.11	TSL:1	c.*695C>G	3_prime_UTR	Exon 22 of 22	ENSP00000349325.6	O60312-1
ATP10A	ENST00000555815.7	TSL:5 MANE Select	c.*695C>G	downstream_gene	N/A	ENSP00000450480.2	O60312-1
ATP10A	ENST00000673805.1		n.*90C>G	downstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over