rs962271

Variant names:

• chr5-160627542-C-T
• rs962271
• NM_025153.3:c.1620+4587G>A

Variant summary

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

The NM_025153.3(ATP10B):​c.1620+4587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,064 control chromosomes in the GnomAD database, including 45,812 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 0.78 (45812 hom., cov: 31)
• Consequence: ATP10B NM_025153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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]

ENSG00000253687 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP10B	NM_025153.3	c.1620+4587G>A		intron_variant	Intron 13 of 25	ENST00000327245.10	NP_079429.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP10B	ENST00000327245.10	c.1620+4587G>A		intron_variant	Intron 13 of 25	1	NM_025153.3	ENSP00000313600.5
ATP10B	ENST00000520108.1	c.444+4587G>A		intron_variant	Intron 2 of 6	1		ENSP00000431081.1
ATP10B	ENST00000642502.1	c.1536+4587G>A		intron_variant	Intron 8 of 20			ENSP00000493802.1
ENSG00000253687	ENST00000523598.1	n.684-11594C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117757 AN: 151946 Hom.: 45776 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.775 AC: 117851 AN: 152064 Hom.: 45812 Cov.: 31 AF XY: 0.775 AC XY: 57612 AN XY: 74318

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.780

Alfa AF: 0.784 Hom.: 6804

Bravo AF: 0.766

Asia WGS AF: 0.763 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.64

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: rs962271; hg19: chr5-160054549;