18-79124480-C-T

Position:

• chr18-79124480-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ATP9B	NM_198531.5	c.559-1787C>T		intron_variant		ENST00000426216.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP9B	ENST00000426216.6	c.559-1787C>T		intron_variant		5	NM_198531.5	A1

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

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.0840

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.0255

Gnomad4 FIN AF: 0.0624

Gnomad4 NFE AF: 0.0925

Gnomad4 OTH AF: 0.113

Alfa AF: 0.108 Hom.: 217

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

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: rs575152; hg19: chr18-76884480;