15-49982814-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024837.4(ATP8B4):c.749-1520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,976 control chromosomes in the GnomAD database, including 21,668 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 0.51 (21668 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

Genes affected

ATP8B4 (HGNC:13536): (ATPase phospholipid transporting 8B4 (putative)) This gene encodes a member of the cation transport ATPase (P-type) family and type IV subfamily. The encoded protein is involved in phospholipid transport in the cell membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B4	NM_024837.4	c.749-1520G>A		intron_variant		ENST00000284509.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B4	ENST00000284509.11	c.749-1520G>A		intron_variant		5	NM_024837.4	P1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77574 AN: 151858 Hom.: 21628 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.511 AC: 77689 AN: 151976 Hom.: 21668 Cov.: 32 AF XY: 0.507 AC XY: 37646 AN XY: 74288

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.504

Alfa AF: 0.436 Hom.: 15111

Bravo AF: 0.536

Asia WGS AF: 0.622 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.9
Dann	Benign	0.71

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: rs8031403; hg19: chr15-50275011;