rs7359209

chr15-25790463-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ATP10A	NM_024490.4	c.450-9240A>G		intron_variant		ENST00000555815.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP10A	ENST00000555815.7	c.450-9240A>G		intron_variant		5	NM_024490.4	P1

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

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.430

Alfa AF: 0.447 Hom.: 21324

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

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

LitVar

Other links and lift over

dbSNP: rs7359209; hg19: chr15-26035610;