rs2076749

Variant names:

• chr15-25863988-A-T
• rs2076749
• ENST00000389967.9:n.-106-786T>A

Variant summary

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

The ENST00000389967.9(ATP10A):​n.-106-786T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,240 control chromosomes in the GnomAD database, including 2,761 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 0.17 (2761 hom., cov: 33)
• Consequence: ATP10A ENST00000389967.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10A	ENST00000389967.9	TSL:1	n.-106-786T>A		intron	N/A	ENSP00000374617.4
	ATP10A	ENST00000619904.1	TSL:5	c.-106-786T>A		intron	N/A	ENSP00000480665.1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26060 AN: 152122 Hom.: 2764 Cov.: 33

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.171 AC: 26052 AN: 152240 Hom.: 2761 Cov.: 33 AF XY: 0.167 AC XY: 12435 AN XY: 74430

African (AFR) AF: 0.0645 AC: 2680 AN: 41562

American (AMR) AF: 0.170 AC: 2596 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3472

East Asian (EAS) AF: 0.00676 AC: 35 AN: 5178

South Asian (SAS) AF: 0.157 AC: 756 AN: 4830

European-Finnish (FIN) AF: 0.178 AC: 1883 AN: 10586

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16596 AN: 68004

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.126 Hom.: 227

Bravo AF: 0.163

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.4
DANN	Benign	0.81
PhyloP100		0.66
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2076749; hg19: chr15-26109135;