rs3924900

Variant names:

• chr4-47547688-A-G
• rs3924900
• NM_020453.4:c.1635+826A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020453.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10D	NM_020453.4	MANE Select	c.1635+826A>G		intron	N/A	NP_065186.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10D	ENST00000273859.8	TSL:1 MANE Select	c.1635+826A>G		intron	N/A	ENSP00000273859.3
	ATP10D	ENST00000503288.6	TSL:2	n.576+826A>G		intron	N/A	ENSP00000421536.1
	ATP10D	ENST00000504445.1	TSL:1	c.*808A>G		downstream_gene	N/A	ENSP00000420909.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.241 AC: 9985 AN: 41474

American (AMR) AF: 0.303 AC: 4636 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1043 AN: 5166

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4818

European-Finnish (FIN) AF: 0.284 AC: 3004 AN: 10572

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14818 AN: 67988

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.230 Hom.: 1965

Bravo AF: 0.239

Asia WGS AF: 0.238 AC: 830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.57
PhyloP100		-0.23
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: rs3924900; hg19: chr4-47549705;