5-160670155-A-T

Variant names:

• chr5-160670155-A-T
• rs1990889
• NM_025153.3:c.675+308T>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.675+308T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 151,994 control chromosomes in the GnomAD database, including 51,165 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 0.82 (51165 hom., cov: 29)
• Consequence: ATP10B NM_025153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.856 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10B	NM_025153.3	MANE Select	c.675+308T>A		intron	N/A	NP_079429.2
	ATP10B	NM_001366652.1		c.675+308T>A		intron	N/A	NP_001353581.1
	ATP10B	NM_001366655.1		c.675+308T>A		intron	N/A	NP_001353584.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP10B	ENST00000327245.10	TSL:1 MANE Select	c.675+308T>A		intron	N/A	ENSP00000313600.5
	ATP10B	ENST00000642502.1		c.591+308T>A		intron	N/A	ENSP00000493802.1
	ATP10B	ENST00000326831.7	TSL:2	n.756+308T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124236 AN: 151876 Hom.: 51143 Cov.: 29

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.818 AC: 124310 AN: 151994 Hom.: 51165 Cov.: 29 AF XY: 0.820 AC XY: 60917 AN XY: 74312

African (AFR) AF: 0.739 AC: 30638 AN: 41434

American (AMR) AF: 0.735 AC: 11211 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3175 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4494 AN: 5152

South Asian (SAS) AF: 0.878 AC: 4223 AN: 4812

European-Finnish (FIN) AF: 0.889 AC: 9407 AN: 10576

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58317 AN: 67974

Other (OTH) AF: 0.821 AC: 1730 AN: 2108

Alfa AF: 0.828 Hom.: 6116

Bravo AF: 0.803

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		-0.20
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: rs1990889; hg19: chr5-160097162;