chr15-25697158-C-G

Position:

• chr15-25697158-C-G

Variant summary

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

The NM_024490.4(ATP10A):​c.2761-2012G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,218 control chromosomes in the GnomAD database, including 911 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 0.10 (911 hom., cov: 33)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

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]

ATP10A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10A	NM_024490.4	c.2761-2012G>C		intron_variant		ENST00000555815.7	NP_077816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000555815.7	c.2761-2012G>C		intron_variant		5	NM_024490.4	ENSP00000450480.2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15578 AN: 152100 Hom.: 912 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.0853

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

GnomAD4 genome AF: 0.102 AC: 15581 AN: 152218 Hom.: 911 Cov.: 33 AF XY: 0.107 AC XY: 7978 AN XY: 74422

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0709

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.0832

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.0835

Alfa AF: 0.0459 Hom.: 30

Bravo AF: 0.0934

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.4
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4906747; hg19: chr15-25942305;