5-160599770-C-T

Position:

• chr5-160599770-C-T

Variant summary

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

The NM_025153.3(ATP10B):​c.3364-800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,072 control chromosomes in the GnomAD database, including 41,076 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 0.73 (41076 hom., cov: 32)
• Consequence: ATP10B NM_025153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

ATP10B (HGNC:13543): (ATPase phospholipid transporting 10B (putative)) Enables glycosylceramide flippase activity and phosphatidylcholine flippase activity. Involved in lysosomal membrane organization. Located in endoplasmic reticulum. Is integral component of lysosomal 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10B	NM_025153.3	c.3364-800G>A		intron_variant		ENST00000327245.10	NP_079429.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP10B	ENST00000327245.10	c.3364-800G>A		intron_variant		1	NM_025153.3	ENSP00000313600.5
ATP10B	ENST00000642502.1	c.3280-800G>A		intron_variant				ENSP00000493802.1

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110845 AN: 151952 Hom.: 41079 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.729 AC: 110886 AN: 152072 Hom.: 41076 Cov.: 32 AF XY: 0.731 AC XY: 54400 AN XY: 74368

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.748

Alfa AF: 0.778 Hom.: 73428

Bravo AF: 0.711

Asia WGS AF: 0.734 AC: 2552 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	13
DANN	Benign	0.71

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: rs4921307; hg19: chr5-160026777;