5-160600675-A-G

Variant names:

• chr5-160600675-A-G
• rs10515813
• NM_025153.3:c.3364-1705T>C

Variant summary

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

The NM_025153.3(ATP10B):​c.3364-1705T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 152,186 control chromosomes in the GnomAD database, including 211 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 0.036 (211 hom., cov: 33)
• Consequence: ATP10B NM_025153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905
• Publications: 4 publications found

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]

MIR3142HG (HGNC:51944): (MIR3142 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10B	NM_025153.3	c.3364-1705T>C		intron_variant	Intron 21 of 25	ENST00000327245.10	NP_079429.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10B	ENST00000327245.10	c.3364-1705T>C		intron_variant	Intron 21 of 25	1	NM_025153.3	ENSP00000313600.5

Frequencies

GnomAD3 genomes AF: 0.0362 AC: 5506 AN: 152066 Hom.: 211 Cov.: 33

Gnomad AFR AF: 0.00693

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0297

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0362 AC: 5506 AN: 152186 Hom.: 211 Cov.: 33 AF XY: 0.0384 AC XY: 2854 AN XY: 74388

African (AFR) AF: 0.00694 AC: 288 AN: 41516

American (AMR) AF: 0.0296 AC: 453 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1067 AN: 5178

South Asian (SAS) AF: 0.0762 AC: 368 AN: 4830

European-Finnish (FIN) AF: 0.0564 AC: 597 AN: 10576

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0354 AC: 2410 AN: 68012

Other (OTH) AF: 0.0408 AC: 86 AN: 2110

Alfa AF: 0.0355 Hom.: 410

Bravo AF: 0.0333

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.65
DANN	Benign	0.33
PhyloP100		-0.91
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: rs10515813; hg19: chr5-160027682;