rs2066707

Variant names:

• chr15-25678646-G-C
• rs2066707
• ENST00000356865:c.*695C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356865(ATP10A):​c.*695C>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 0.633 in 152,066 control chromosomes in the GnomAD database, including 30,940 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 0.63 (30938 hom., cov: 33)
  • Exomes 𝑓: 0.63 (2 hom.)
• Consequence: ATP10A ENST00000356865 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10A	NM_024490.4	c.*695C>G		downstream_gene_variant		ENST00000555815.7	NP_077816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10A	ENST00000356865	c.*695C>G		3_prime_UTR_variant	Exon 22 of 22	1		ENSP00000349325.6
ATP10A	ENST00000555815.7	c.*695C>G		downstream_gene_variant		5	NM_024490.4	ENSP00000450480.2
ATP10A	ENST00000673805.1	n.*90C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96095 AN: 151940 Hom.: 30892 Cov.: 33

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.629

GnomAD4 exome AF: 0.625 AC: 5 AN: 8 Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.633 AC: 96197 AN: 152058 Hom.: 30938 Cov.: 33 AF XY: 0.628 AC XY: 46672 AN XY: 74312

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.626

Alfa AF: 0.624 Hom.: 3684

Bravo AF: 0.635

Asia WGS AF: 0.464 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.43

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: rs2066707; hg19: chr15-25923793;