rs11638841

Positions:

• chr15-50124410-C-G

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-42-17402G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,796 control chromosomes in the GnomAD database, including 8,159 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 0.31 (8159 hom., cov: 32)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.807

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=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B4	XM_011522056.4	c.-42-17402G>C		intron_variant
ATP8B4	XM_017022587.3	c.-42-17402G>C		intron_variant
ATP8B4	XM_047433096.1	c.-42-17402G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B4	ENST00000558829.1	c.-42-17402G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46623 AN: 151678 Hom.: 8157 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.307 AC: 46630 AN: 151796 Hom.: 8159 Cov.: 32 AF XY: 0.308 AC XY: 22867 AN XY: 74154

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.332

Alfa AF: 0.347 Hom.: 1228

Bravo AF: 0.290

Asia WGS AF: 0.285 AC: 996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11638841; hg19: chr15-50416607;