15-25678340-T-C

Variant names:

• chr15-25678340-T-C
• rs2066710
• ENST00000356865.11:c.*1001A>G

Variant summary

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

The ENST00000356865.11(ATP10A):​c.*1001A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,782 control chromosomes in the GnomAD database, including 19,507 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 0.50 (19495 hom., cov: 31)
  • Exomes 𝑓: 0.55 (12 hom.)
• Consequence: ATP10A ENST00000356865.11 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000356865.11. 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	ENST00000356865.11	TSL:1	c.*1001A>G		3_prime_UTR	Exon 22 of 22	ENSP00000349325.6	O60312-1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76106 AN: 151598 Hom.: 19465 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.465

GnomAD4 exome AF: 0.547 AC: 35 AN: 64 Hom.: 12 Cov.: 0 AF XY: 0.620 AC XY: 31 AN XY: 50

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.545 AC: 24 AN: 44

Other (OTH) AF: 0.500 AC: 5 AN: 10

GnomAD4 genome AF: 0.502 AC: 76188 AN: 151718 Hom.: 19495 Cov.: 31 AF XY: 0.501 AC XY: 37087 AN XY: 74092

African (AFR) AF: 0.597 AC: 24674 AN: 41362

American (AMR) AF: 0.491 AC: 7494 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1516 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1943 AN: 5126

South Asian (SAS) AF: 0.441 AC: 2106 AN: 4778

European-Finnish (FIN) AF: 0.492 AC: 5161 AN: 10496

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31690 AN: 67916

Other (OTH) AF: 0.465 AC: 981 AN: 2110

Alfa AF: 0.474 Hom.: 29150

Bravo AF: 0.503

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.49
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2066710;

hg19: chr15-25923487;