5-160888626-A-G

Variant names:

• chr5-160888626-A-G
• rs17427250
• XM_011534468.3:c.-215+40596T>C

Variant summary

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

The XM_011534468.3(ATP10B):​c.-215+40596T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,206 control chromosomes in the GnomAD database, including 1,962 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 0.15 (1962 hom., cov: 33)
• Consequence: ATP10B XM_011534468.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10B	XM_011534468.3	c.-215+40596T>C		intron_variant	Intron 1 of 24		XP_011532770.1
ATP10B	XM_047416994.1	c.-215+19926T>C		intron_variant	Intron 2 of 25		XP_047272950.1
ATP10B	XM_017009252.2	c.-215+40596T>C		intron_variant	Intron 1 of 24		XP_016864741.1
ATP10B	XM_047416995.1	c.-215+40596T>C		intron_variant	Intron 1 of 23		XP_047272951.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22606 AN: 152088 Hom.: 1955 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.149 AC: 22654 AN: 152206 Hom.: 1962 Cov.: 33 AF XY: 0.147 AC XY: 10971 AN XY: 74420

African (AFR) AF: 0.226 AC: 9374 AN: 41530

American (AMR) AF: 0.110 AC: 1678 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3468

East Asian (EAS) AF: 0.121 AC: 624 AN: 5168

South Asian (SAS) AF: 0.136 AC: 655 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1340 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8104 AN: 68008

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.0804 Hom.: 147

Bravo AF: 0.153

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.54
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17427250; hg19: chr5-160315633;