15-25803910-A-G

Position:

• chr15-25803910-A-G

Variant summary

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

The NM_024490.4(ATP10A):​c.450-22687T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,032 control chromosomes in the GnomAD database, including 6,599 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 0.27 (6599 hom., cov: 34)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP10A	NM_024490.4	c.450-22687T>C		intron_variant		ENST00000555815.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP10A	ENST00000555815.7	c.450-22687T>C		intron_variant		5	NM_024490.4	P1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41429 AN: 151914 Hom.: 6589 Cov.: 34

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.273 AC: 41475 AN: 152032 Hom.: 6599 Cov.: 34 AF XY: 0.268 AC XY: 19902 AN XY: 74318

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.0377

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.282

Alfa AF: 0.243 Hom.: 872

Bravo AF: 0.284

Asia WGS AF: 0.125 AC: 435 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	2.3
DANN	Benign	0.26
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs4906777; hg19: chr15-26049057;