5-160769084-A-T

Position:

• chr5-160769084-A-T

Variant summary

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

The NM_025153.3(ATP10B):​c.-331+16475T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,126 control chromosomes in the GnomAD database, including 3,655 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 0.20 (3655 hom., cov: 32)
• Consequence: ATP10B NM_025153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP10B	NM_025153.3	c.-331+16475T>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.-331+16475T>A		intron_variant		1	NM_025153.3	ENSP00000313600	P1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30386 AN: 152006 Hom.: 3641 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.200 AC: 30433 AN: 152126 Hom.: 3655 Cov.: 32 AF XY: 0.208 AC XY: 15443 AN XY: 74368

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.217

Alfa AF: 0.166 Hom.: 272

Bravo AF: 0.218

Asia WGS AF: 0.381 AC: 1323 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	2.5
DANN	Benign	0.74

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: rs4476766; hg19: chr5-160196091;