NM_020453.4:c.3942-409G>A

Variant names:

• chr4-47590633-G-A
• rs4558836
• NM_020453.4:c.3942-409G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020453.4(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 NM_020453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 2 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 -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 rank	MANE	Protein	UniProt
ATP10D	NM_020453.4	c.3942-409G>A		intron_variant	Intron 22 of 22	ENST00000273859.8	NP_065186.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10D	ENST00000273859.8	c.3942-409G>A		intron_variant	Intron 22 of 22	1	NM_020453.4	ENSP00000273859.3
ATP10D	ENST00000503288.6	n.*1624-409G>A		intron_variant	Intron 15 of 15	2		ENSP00000421536.1
ATP10D	ENST00000505277.1	n.316-409G>A		intron_variant	Intron 3 of 3	5
ATP10D	ENST00000505476.5	n.520-409G>A		intron_variant	Intron 4 of 4	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

African (AFR) AF: 0.145 AC: 6017 AN: 41464

American (AMR) AF: 0.151 AC: 2310 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0963 AC: 334 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2476 AN: 5136

South Asian (SAS) AF: 0.121 AC: 582 AN: 4818

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0900 AC: 6113 AN: 67960

Other (OTH) AF: 0.129 AC: 273 AN: 2114

Alfa AF: 0.106 Hom.: 1978

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
PhyloP100		0.31
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: rs4558836; hg19: chr4-47592650;