chr4-47580370-A-C

Position:

• chr4-47580370-A-C

Variant summary

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

The NM_020453.4(ATP10D):​c.3568-28A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 1,550,370 control chromosomes in the GnomAD database, including 457,310 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. There are indicators that this mutation may affect the branch point..

• Frequency:
  • Genomes: 𝑓 0.76 (43858 hom., cov: 31)
  • Exomes 𝑓: 0.77 (413452 hom.)
• Consequence: ATP10D NM_020453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

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]

ATP10D (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: This place is a probable branch point but likely benign (scored 1 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10D	NM_020453.4	c.3568-28A>C		intron_variant		ENST00000273859.8	NP_065186.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10D	ENST00000273859.8	c.3568-28A>C		intron_variant		1	NM_020453.4	ENSP00000273859.3
ATP10D	ENST00000503288.6	n.*1250-28A>C		intron_variant		2		ENSP00000421536.1
ATP10D	ENST00000505476.5	n.146-28A>C		intron_variant		4
ATP10D	ENST00000512393.1	n.-29A>C		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115226 AN: 151848 Hom.: 43840 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.747

GnomAD3 exomes AF: 0.757 AC: 189927 AN: 250922 Hom.: 72102 AF XY: 0.756 AC XY: 102479 AN XY: 135634

Gnomad AFR exome AF: 0.767

Gnomad AMR exome AF: 0.753

Gnomad ASJ exome AF: 0.682

Gnomad EAS exome AF: 0.696

Gnomad SAS exome AF: 0.744

Gnomad FIN exome AF: 0.786

Gnomad NFE exome AF: 0.772

Gnomad OTH exome AF: 0.740

GnomAD4 exome AF: 0.768 AC: 1074315 AN: 1398404 Hom.: 413452 Cov.: 23 AF XY: 0.767 AC XY: 536629 AN XY: 699658

Gnomad4 AFR exome AF: 0.762

Gnomad4 AMR exome AF: 0.748

Gnomad4 ASJ exome AF: 0.683

Gnomad4 EAS exome AF: 0.742

Gnomad4 SAS exome AF: 0.741

Gnomad4 FIN exome AF: 0.780

Gnomad4 NFE exome AF: 0.775

Gnomad4 OTH exome AF: 0.760

GnomAD4 genome AF: 0.759 AC: 115298 AN: 151966 Hom.: 43858 Cov.: 31 AF XY: 0.755 AC XY: 56074 AN XY: 74262

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.750

Alfa AF: 0.759 Hom.: 26432

Bravo AF: 0.755

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.50
BranchPoint Hunter		1.0

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: rs2351791; hg19: chr4-47582387;