15-25863988-A-T

Position:

• chr15-25863988-A-T

Variant summary

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

The ENST00000619904.1(ATP10A):​c.-106-786T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,240 control chromosomes in the GnomAD database, including 2,761 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 0.17 (2761 hom., cov: 33)
• Consequence: ATP10A ENST00000619904.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10A	XM_005268261.5	c.-106-786T>A		intron_variant			XP_005268318.1
ATP10A	XM_011521826.3	c.-464T>A		upstream_gene_variant			XP_011520128.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000389967.9	n.-106-786T>A		intron_variant		1		ENSP00000374617.4
ATP10A	ENST00000619904.1	c.-106-786T>A		intron_variant		5		ENSP00000480665.1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26060 AN: 152122 Hom.: 2764 Cov.: 33

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.171 AC: 26052 AN: 152240 Hom.: 2761 Cov.: 33 AF XY: 0.167 AC XY: 12435 AN XY: 74430

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.00676

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.211

Alfa AF: 0.126 Hom.: 227

Bravo AF: 0.163

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2076749; hg19: chr15-26109135;