XM_011534468.3:c.-215+40629T>C

Variant names:

• chr5-160888593-A-G
• rs11956144
• XM_011534468.3:c.-215+40629T>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+40629T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,226 control chromosomes in the GnomAD database, including 1,799 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 0.14 (1799 hom., cov: 33)
• Consequence: ATP10B XM_011534468.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10B	XM_011534468.3	c.-215+40629T>C		intron_variant	Intron 1 of 24		XP_011532770.1
ATP10B	XM_047416994.1	c.-215+19959T>C		intron_variant	Intron 2 of 25		XP_047272950.1
ATP10B	XM_017009252.2	c.-215+40629T>C		intron_variant	Intron 1 of 24		XP_016864741.1
ATP10B	XM_047416995.1	c.-215+40629T>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: 0.144 AC: 21870 AN: 152108 Hom.: 1793 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.144 AC: 21905 AN: 152226 Hom.: 1799 Cov.: 33 AF XY: 0.142 AC XY: 10585 AN XY: 74428

African (AFR) AF: 0.211 AC: 8753 AN: 41532

American (AMR) AF: 0.109 AC: 1672 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3470

East Asian (EAS) AF: 0.118 AC: 609 AN: 5178

South Asian (SAS) AF: 0.118 AC: 566 AN: 4814

European-Finnish (FIN) AF: 0.126 AC: 1339 AN: 10596

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8092 AN: 68020

Other (OTH) AF: 0.135 AC: 286 AN: 2116

Alfa AF: 0.135 Hom.: 261

Bravo AF: 0.148

Asia WGS AF: 0.137 AC: 480 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	4.1
DANN	Benign	0.71
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs11956144; hg19: chr5-160315600;