rs13139804

Variant names:

• chr4-47542464-A-G
• rs13139804
• NM_020453.4:c.1397-4160A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020453.4(ATP10D):​c.1397-4160A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,724 control chromosomes in the GnomAD database, including 11,967 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 0.39 (11967 hom., cov: 31)
• Consequence: ATP10D NM_020453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10D	NM_020453.4	c.1397-4160A>G		intron_variant	Intron 9 of 22	ENST00000273859.8	NP_065186.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10D	ENST00000273859.8	c.1397-4160A>G		intron_variant	Intron 9 of 22	1	NM_020453.4	ENSP00000273859.3
ATP10D	ENST00000504445.1	c.1352-4160A>G		intron_variant	Intron 9 of 9	1		ENSP00000420909.1
ATP10D	ENST00000503288.6	n.338-4160A>G		intron_variant	Intron 2 of 15	2		ENSP00000421536.1

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58983 AN: 151608 Hom.: 11962 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.389 AC: 59007 AN: 151724 Hom.: 11967 Cov.: 31 AF XY: 0.397 AC XY: 29397 AN XY: 74136

African (AFR) AF: 0.292 AC: 12064 AN: 41342

American (AMR) AF: 0.413 AC: 6292 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1539 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1179 AN: 5138

South Asian (SAS) AF: 0.479 AC: 2304 AN: 4812

European-Finnish (FIN) AF: 0.525 AC: 5520 AN: 10512

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.425 AC: 28890 AN: 67900

Other (OTH) AF: 0.360 AC: 759 AN: 2108

Alfa AF: 0.400 Hom.: 7554

Bravo AF: 0.372

Asia WGS AF: 0.347 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	10
DANN	Benign	0.79
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13139804; hg19: chr4-47544481;