15-25864838-C-T

Variant names:

• chr15-25864838-C-T
• rs2076748
• ENST00000389967.9:n.-107+177G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000389967.9(ATP10A):​n.-107+177G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,976 control chromosomes in the GnomAD database, including 33,084 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 0.63 (33084 hom., cov: 32)
• Consequence: ATP10A ENST00000389967.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.776
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000389967.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10A	ENST00000389967.9	TSL:1	n.-107+177G>A		intron	N/A	ENSP00000374617.4
	ATP10A	ENST00000619904.1	TSL:5	c.-107+177G>A		intron	N/A	ENSP00000480665.1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94993 AN: 151858 Hom.: 33089 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.625 AC: 95013 AN: 151976 Hom.: 33084 Cov.: 32 AF XY: 0.626 AC XY: 46513 AN XY: 74260

African (AFR) AF: 0.295 AC: 12230 AN: 41454

American (AMR) AF: 0.722 AC: 11039 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2576 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3179 AN: 5106

South Asian (SAS) AF: 0.512 AC: 2460 AN: 4804

European-Finnish (FIN) AF: 0.796 AC: 8430 AN: 10588

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52793 AN: 67954

Other (OTH) AF: 0.674 AC: 1419 AN: 2106

Alfa AF: 0.707 Hom.: 64552

Bravo AF: 0.614

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.54
PhyloP100		0.78
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2076748; hg19: chr15-26109985;