rs3924900

Positions:

• chr4-47547688-A-G

Variant summary

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

The NM_020453.4(ATP10D):​c.1635+826A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,090 control chromosomes in the GnomAD database, including 4,323 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 0.24 (4321 hom., cov: 32)
  • Exomes 𝑓: 0.67 (2 hom.)
• Consequence: ATP10D NM_020453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP10D	NM_020453.4	c.1635+826A>G		intron_variant		ENST00000273859.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP10D	ENST00000273859.8	c.1635+826A>G		intron_variant		1	NM_020453.4	P1
ATP10D	ENST00000503288.6	c.577+826A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36185 AN: 151966 Hom.: 4315 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 2 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.238 AC: 36226 AN: 152084 Hom.: 4321 Cov.: 32 AF XY: 0.243 AC XY: 18032 AN XY: 74342

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.218

Alfa AF: 0.232 Hom.: 1737

Bravo AF: 0.239

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.57

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: rs3924900; hg19: chr4-47549705;