NM_025153.3:c.1620+4587G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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]

ENSG00000253687 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025153.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10B	NM_025153.3	MANE Select	c.1620+4587G>A		intron	N/A	NP_079429.2	O94823-1
	ATP10B	NM_001366652.1		c.1620+4587G>A		intron	N/A	NP_001353581.1	O94823-1
	ATP10B	NM_001366655.1		c.1620+4587G>A		intron	N/A	NP_001353584.1	O94823-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10B	ENST00000327245.10	TSL:1 MANE Select	c.1620+4587G>A		intron	N/A	ENSP00000313600.5	O94823-1
	ATP10B	ENST00000520108.1	TSL:1	c.444+4587G>A		intron	N/A	ENSP00000431081.1	Q2YDW8
	ATP10B	ENST00000943128.1		c.1620+4587G>A		intron	N/A	ENSP00000613187.1

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

African (AFR) AF: 0.786 AC: 32608 AN: 41494

American (AMR) AF: 0.690 AC: 10532 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2816 AN: 3468

East Asian (EAS) AF: 0.840 AC: 4334 AN: 5160

South Asian (SAS) AF: 0.781 AC: 3752 AN: 4804

European-Finnish (FIN) AF: 0.800 AC: 8463 AN: 10574

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.775 AC: 52715 AN: 67984

Other (OTH) AF: 0.780 AC: 1644 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-1.5
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: rs962271; hg19: chr5-160054549;