chr18-79124480-C-T

Variant names:

• chr18-79124480-C-T
• rs575152
• NM_198531.5:c.559-1787C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198531.5(ATP9B):​c.559-1787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,292 control chromosomes in the GnomAD database, including 1,925 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 0.13 (1925 hom., cov: 33)
• Consequence: ATP9B NM_198531.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 2 publications found

Genes affected

ATP9B (HGNC:13541): (ATPase phospholipid transporting 9B (putative)) Predicted to enable ATPase-coupled intramembrane lipid transporter activity. Predicted to be involved in endocytosis; phospholipid translocation; and retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Located in perinuclear region of cytoplasm and trans-Golgi network. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP9B	NM_198531.5	c.559-1787C>T		intron_variant	Intron 4 of 29	ENST00000426216.6	NP_940933.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP9B	ENST00000426216.6	c.559-1787C>T		intron_variant	Intron 4 of 29	5	NM_198531.5	ENSP00000398076.2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20055 AN: 152174 Hom.: 1915 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0841

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0190

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0926

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.132 AC: 20083 AN: 152292 Hom.: 1925 Cov.: 33 AF XY: 0.128 AC XY: 9514 AN XY: 74494

African (AFR) AF: 0.267 AC: 11084 AN: 41528

American (AMR) AF: 0.0840 AC: 1285 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5186

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4830

European-Finnish (FIN) AF: 0.0624 AC: 663 AN: 10630

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0925 AC: 6294 AN: 68026

Other (OTH) AF: 0.113 AC: 239 AN: 2110

Alfa AF: 0.109 Hom.: 381

Bravo AF: 0.142

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.67
PhyloP100		1.1
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: rs575152; hg19: chr18-76884480;