rs2044313

Variant names:

• chr15-25838720-C-T
• rs2044313
• NM_024490.4:c.449+23928G>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.449+23928G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,104 control chromosomes in the GnomAD database, including 32,334 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 0.63 (32334 hom., cov: 32)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10A	NM_024490.4	c.449+23928G>A		intron_variant	Intron 1 of 20	ENST00000555815.7	NP_077816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000555815.7	c.449+23928G>A		intron_variant	Intron 1 of 20	5	NM_024490.4	ENSP00000450480.2

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95219 AN: 151986 Hom.: 32317 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.626 AC: 95273 AN: 152104 Hom.: 32334 Cov.: 32 AF XY: 0.634 AC XY: 47113 AN XY: 74368

African (AFR) AF: 0.352 AC: 14565 AN: 41434

American (AMR) AF: 0.732 AC: 11195 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2267 AN: 3472

East Asian (EAS) AF: 0.913 AC: 4727 AN: 5178

South Asian (SAS) AF: 0.744 AC: 3588 AN: 4824

European-Finnish (FIN) AF: 0.778 AC: 8238 AN: 10588

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48489 AN: 68010

Other (OTH) AF: 0.647 AC: 1364 AN: 2108

Alfa AF: 0.689 Hom.: 20155

Bravo AF: 0.613

Asia WGS AF: 0.810 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.62
PhyloP100		-0.23
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: rs2044313; hg19: chr15-26083867;