rs4906777

Variant names:

• chr15-25803910-A-G
• rs4906777
• NM_024490.4:c.450-22687T>C

Your query was ambiguous. Multiple possible variants found:

• chr15-25803910-A-G
• chr15-25803910-A-T

Variant summary

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

The NM_024490.4(ATP10A):​c.450-22687T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,032 control chromosomes in the GnomAD database, including 6,599 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 0.27 (6599 hom., cov: 34)
• Consequence: ATP10A NM_024490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10A	NM_024490.4	c.450-22687T>C		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.450-22687T>C		intron_variant	Intron 1 of 20	5	NM_024490.4	ENSP00000450480.2

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41429 AN: 151914 Hom.: 6589 Cov.: 34

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.273 AC: 41475 AN: 152032 Hom.: 6599 Cov.: 34 AF XY: 0.268 AC XY: 19902 AN XY: 74318

African (AFR) AF: 0.441 AC: 18298 AN: 41448

American (AMR) AF: 0.214 AC: 3270 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 958 AN: 3464

East Asian (EAS) AF: 0.0377 AC: 195 AN: 5168

South Asian (SAS) AF: 0.186 AC: 894 AN: 4818

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10572

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15236 AN: 67966

Other (OTH) AF: 0.282 AC: 597 AN: 2114

Alfa AF: 0.299 Hom.: 3385

Bravo AF: 0.284

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.26
PhyloP100		-0.067
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs4906777; hg19: chr15-26049057;