rs10938494

chr4-47561431-G-A

Variant summary

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

The NM_020453.4(ATP10D):c.2668+356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,102 control chromosomes in the GnomAD database, including 3,650 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 0.22 (3650 hom., cov: 32)
• Consequence: ATP10D NM_020453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

Genes affected

ATP10D (HGNC:13549): (ATPase phospholipid transporting 10D (putative)) Enables glycosylceramide flippase activity. Predicted to be involved in phospholipid translocation. Located in endoplasmic reticulum; nucleoplasm; and plasma membrane. Is integral component of plasma membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP10D	NM_020453.4	c.2668+356G>A		intron_variant		ENST00000273859.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP10D	ENST00000273859.8	c.2668+356G>A		intron_variant		1	NM_020453.4	P1
ATP10D	ENST00000503288.6	c.*350+356G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32931 AN: 151982 Hom.: 3648 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.217 AC: 32954 AN: 152102 Hom.: 3650 Cov.: 32 AF XY: 0.219 AC XY: 16274 AN XY: 74358

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.246

Alfa AF: 0.220 Hom.: 6099

Bravo AF: 0.221

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	2.0
Dann	Benign	0.79

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: rs10938494; hg19: chr4-47563448;