rs4906796

Variant names:

• chr15-25864661-C-G
• rs4906796
• ENST00000389967.9:n.-107+354G>C

Variant summary

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

The ENST00000389967.9(ATP10A):​n.-107+354G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,240 control chromosomes in the GnomAD database, including 60,567 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 0.89 (60567 hom., cov: 33)
• Consequence: ATP10A ENST00000389967.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000389967.9. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10A	ENST00000389967.9	TSL:1	n.-107+354G>C		intron	N/A	ENSP00000374617.4
	ATP10A	ENST00000619904.1	TSL:5	c.-107+354G>C		intron	N/A	ENSP00000480665.1

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135398 AN: 152120 Hom.: 60524 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.890 AC: 135503 AN: 152240 Hom.: 60567 Cov.: 33 AF XY: 0.891 AC XY: 66351 AN XY: 74428

African (AFR) AF: 0.797 AC: 33066 AN: 41506

American (AMR) AF: 0.932 AC: 14264 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3281 AN: 3472

East Asian (EAS) AF: 0.940 AC: 4862 AN: 5172

South Asian (SAS) AF: 0.861 AC: 4158 AN: 4828

European-Finnish (FIN) AF: 0.953 AC: 10118 AN: 10616

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62658 AN: 68020

Other (OTH) AF: 0.910 AC: 1925 AN: 2116

Alfa AF: 0.898 Hom.: 7644

Bravo AF: 0.886

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4906796; hg19: chr15-26109808;