chr15-25743068-C-T

Position:

• chr15-25743068-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.655-6927G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,076 control chromosomes in the GnomAD database, including 7,984 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 0.29 (7984 hom., cov: 32)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10A	NM_024490.4	c.655-6927G>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.655-6927G>A		intron_variant		5	NM_024490.4	ENSP00000450480	P1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44068 AN: 151954 Hom.: 7984 Cov.: 32

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.290 AC: 44072 AN: 152076 Hom.: 7984 Cov.: 32 AF XY: 0.292 AC XY: 21681 AN XY: 74328

Gnomad4 AFR AF: 0.0713

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.297

Alfa AF: 0.368 Hom.: 21887

Bravo AF: 0.259

Asia WGS AF: 0.346 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.45

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: rs12901627; hg19: chr15-25988215;