5-160600675-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• 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
ATP10B	ENST00000642502.1	c.3280-1705T>C		intron_variant	Intron 16 of 20			ENSP00000493802.1

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

Gnomad4 AFR AF: 0.00694

Gnomad4 AMR AF: 0.0296

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.0762

Gnomad4 FIN AF: 0.0564

Gnomad4 NFE AF: 0.0354

Gnomad4 OTH AF: 0.0408

Alfa AF: 0.0342 Hom.: 113

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

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: rs10515813; hg19: chr5-160027682;