chr15-25744629-C-T

Variant names:

• chr15-25744629-C-T
• rs12717755
• NM_024490.4:c.655-8488G>A

Variant summary

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

The NM_024490.4(ATP10A):​c.655-8488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,968 control chromosomes in the GnomAD database, including 15,511 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 0.45 (15511 hom., cov: 33)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024490.4. 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
	ATP10A	NM_024490.4	MANE Select	c.655-8488G>A		intron	N/A	NP_077816.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10A	ENST00000555815.7	TSL:5 MANE Select	c.655-8488G>A		intron	N/A	ENSP00000450480.2
	ATP10A	ENST00000356865.11	TSL:1	c.655-8488G>A		intron	N/A	ENSP00000349325.6
	ATP10A	ENST00000673747.1		c.655-8488G>A		intron	N/A	ENSP00000501230.1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67966 AN: 151850 Hom.: 15495 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.448 AC: 68025 AN: 151968 Hom.: 15511 Cov.: 33 AF XY: 0.451 AC XY: 33486 AN XY: 74268

African (AFR) AF: 0.500 AC: 20703 AN: 41440

American (AMR) AF: 0.478 AC: 7287 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1080 AN: 3466

East Asian (EAS) AF: 0.612 AC: 3167 AN: 5172

South Asian (SAS) AF: 0.504 AC: 2420 AN: 4806

European-Finnish (FIN) AF: 0.443 AC: 4671 AN: 10542

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27563 AN: 67970

Other (OTH) AF: 0.417 AC: 881 AN: 2112

Alfa AF: 0.405 Hom.: 17994

Bravo AF: 0.446

Asia WGS AF: 0.541 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.51
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12717755; hg19: chr15-25989776;