15-25678340-T-C

Position:

• chr15-25678340-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10A	XM_011521828.3	c.4242+1259A>G		intron_variant			XP_011520130.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000356865.11	c.*1001A>G		3_prime_UTR_variant	22/22	1		ENSP00000349325	P1

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

Gnomad4 AFR exome AF: 0.833

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.465

Alfa AF: 0.471 Hom.: 22945

Bravo AF: 0.503

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs2066710; hg19: chr15-25923487;