15-25672819-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
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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

Other links and lift over

dbSNP: rs2930629; hg19: chr15-25917966;