chr15-25672819-G-A

Position:

• chr15-25672819-G-A

Variant summary

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

The XM_011521828.3(ATP10A):​c.*585C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,932 control chromosomes in the GnomAD database, including 19,667 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 0.49 (19667 hom., cov: 31)
• Consequence: ATP10A XM_011521828.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10A	XM_011521828.3	c.*585C>T		3_prime_UTR_variant	22/22		XP_011520130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73958 AN: 151814 Hom.: 19656 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.487 AC: 73991 AN: 151932 Hom.: 19667 Cov.: 31 AF XY: 0.484 AC XY: 35940 AN XY: 74250

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.526

Alfa AF: 0.563 Hom.: 20664

Bravo AF: 0.487

Asia WGS AF: 0.337 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2930629; hg19: chr15-25917966;