rs4558836

Positions:

• chr4-47590633-G-A

Variant summary

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

The ENST00000273859.8(ATP10D):​c.3942-409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,022 control chromosomes in the GnomAD database, including 1,695 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 0.13 (1695 hom., cov: 32)
• Consequence: ATP10D ENST00000273859.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10D	NM_020453.4	c.3942-409G>A		intron_variant		ENST00000273859.8	NP_065186.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10D	ENST00000273859.8	c.3942-409G>A		intron_variant		1	NM_020453.4	ENSP00000273859	P1
ATP10D	ENST00000503288.6	c.*1624-409G>A		intron_variant, NMD_transcript_variant		2		ENSP00000421536
ATP10D	ENST00000505277.1	n.316-409G>A		intron_variant, non_coding_transcript_variant		5
ATP10D	ENST00000505476.5	n.520-409G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19376 AN: 151904 Hom.: 1695 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.128 AC: 19395 AN: 152022 Hom.: 1695 Cov.: 32 AF XY: 0.130 AC XY: 9662 AN XY: 74320

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0900

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0978 Hom.: 355

Bravo AF: 0.137

Asia WGS AF: 0.258 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.59

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: rs4558836; hg19: chr4-47592650;