15-25744629-C-T

Position:

• chr15-25744629-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024490.4(ATP10A):​c.655-8488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,968 control chromosomes in the GnomAD database, including 15,511 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 0.45 (15511 hom., cov: 33)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10A	NM_024490.4	c.655-8488G>A		intron_variant		ENST00000555815.7	NP_077816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000555815.7	c.655-8488G>A		intron_variant		5	NM_024490.4	ENSP00000450480	P1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67966 AN: 151850 Hom.: 15495 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.448 AC: 68025 AN: 151968 Hom.: 15511 Cov.: 33 AF XY: 0.451 AC XY: 33486 AN XY: 74268

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.417

Alfa AF: 0.402 Hom.: 14368

Bravo AF: 0.446

Asia WGS AF: 0.541 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.51

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: rs12717755; hg19: chr15-25989776;