rs7359209

Variant names:

• chr15-25790463-T-C
• rs7359209
• NM_024490.4:c.450-9240A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024490.4(ATP10A):​c.450-9240A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,986 control chromosomes in the GnomAD database, including 14,692 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 0.44 (14692 hom., cov: 32)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10A	NM_024490.4	c.450-9240A>G		intron_variant	Intron 1 of 20	ENST00000555815.7	NP_077816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000555815.7	c.450-9240A>G		intron_variant	Intron 1 of 20	5	NM_024490.4	ENSP00000450480.2

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66453 AN: 151868 Hom.: 14662 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.423

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.438 AC: 66536 AN: 151986 Hom.: 14692 Cov.: 32 AF XY: 0.443 AC XY: 32919 AN XY: 74282

African (AFR) AF: 0.378 AC: 15681 AN: 41470

American (AMR) AF: 0.476 AC: 7269 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2181 AN: 5136

South Asian (SAS) AF: 0.553 AC: 2658 AN: 4808

European-Finnish (FIN) AF: 0.500 AC: 5281 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30690 AN: 67964

Other (OTH) AF: 0.430 AC: 908 AN: 2112

Alfa AF: 0.446 Hom.: 26650

Bravo AF: 0.431

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7359209; hg19: chr15-26035610;