rs13106975

chr4-47549846-T-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+2984T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,032 control chromosomes in the GnomAD database, including 4,003 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 0.23 (4003 hom., cov: 33)
• Consequence: ATP10D NM_020453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP10D	NM_020453.4	c.1635+2984T>G		intron_variant		ENST00000273859.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP10D	ENST00000273859.8	c.1635+2984T>G		intron_variant		1	NM_020453.4	P1
ATP10D	ENST00000503288.6	c.577+2984T>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34566 AN: 151916 Hom.: 4002 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.227 AC: 34587 AN: 152032 Hom.: 4003 Cov.: 33 AF XY: 0.230 AC XY: 17058 AN XY: 74298

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.254

Alfa AF: 0.236 Hom.: 4207

Bravo AF: 0.230

Asia WGS AF: 0.237 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.9
Dann	Benign	0.76

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: rs13106975; hg19: chr4-47551863;