chr15-25672819-G-A

Variant names:

• chr15-25672819-G-A
• rs2930629
• XM_011521828.3:c.*585C>T

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATP10A	XM_011521828.3	c.*585C>T		3_prime_UTR_variant	Exon 22 of 22		XP_011520130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.278 AC: 11511 AN: 41424

American (AMR) AF: 0.618 AC: 9449 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1492 AN: 5146

South Asian (SAS) AF: 0.433 AC: 2086 AN: 4814

European-Finnish (FIN) AF: 0.518 AC: 5467 AN: 10546

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40043 AN: 67946

Other (OTH) AF: 0.526 AC: 1106 AN: 2102

Alfa AF: 0.563 Hom.: 24598

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
PhyloP100		-0.24

Splicing

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

Publications

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Other links and lift over

dbSNP: rs2930629; hg19: chr15-25917966;