5-160599770-C-T

Variant names:

• chr5-160599770-C-T
• rs4921307
• NM_025153.3:c.3364-800G>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.3364-800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,072 control chromosomes in the GnomAD database, including 41,076 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 0.73 (41076 hom., cov: 32)
• Consequence: ATP10B NM_025153.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• 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]

MIR3142HG (HGNC:51944): (MIR3142 host gene)

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 (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.3364-800G>A		intron	N/A	NP_079429.2	O94823-1
	ATP10B	NM_001366652.1		c.3364-800G>A		intron	N/A	NP_001353581.1	O94823-1
	ATP10B	NM_001366655.1		c.3364-800G>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.3364-800G>A		intron	N/A	ENSP00000313600.5	O94823-1
	ATP10B	ENST00000943128.1		c.3364-800G>A		intron	N/A	ENSP00000613187.1
	ATP10B	ENST00000642502.1		c.3280-800G>A		intron	N/A	ENSP00000493802.1	A0A2R8YDI5

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110845 AN: 151952 Hom.: 41079 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.729 AC: 110886 AN: 152072 Hom.: 41076 Cov.: 32 AF XY: 0.731 AC XY: 54400 AN XY: 74368

African (AFR) AF: 0.595 AC: 24629 AN: 41424

American (AMR) AF: 0.683 AC: 10443 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2837 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4351 AN: 5178

South Asian (SAS) AF: 0.774 AC: 3732 AN: 4824

European-Finnish (FIN) AF: 0.827 AC: 8753 AN: 10588

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53607 AN: 67988

Other (OTH) AF: 0.748 AC: 1579 AN: 2112

Alfa AF: 0.764 Hom.: 144487

Bravo AF: 0.711

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	13
DANN	Benign	0.71
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: rs4921307; hg19: chr5-160026777;