15-50124410-C-G

Variant names:

• chr15-50124410-C-G
• rs11638841
• ENST00000895127.1:c.-42-17402G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558829.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000895127.1		c.-42-17402G>C		intron	N/A	ENSP00000565186.1
	ATP8B4	ENST00000966552.1		c.-42-17402G>C		intron	N/A	ENSP00000636611.1
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-17402G>C		intron	N/A	ENSP00000453539.1	H0YMB5

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

African (AFR) AF: 0.126 AC: 5211 AN: 41472

American (AMR) AF: 0.301 AC: 4585 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1452 AN: 3464

East Asian (EAS) AF: 0.308 AC: 1587 AN: 5154

South Asian (SAS) AF: 0.339 AC: 1636 AN: 4820

European-Finnish (FIN) AF: 0.420 AC: 4413 AN: 10506

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26566 AN: 67824

Other (OTH) AF: 0.332 AC: 699 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		0.81

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11638841;

hg19: chr15-50416607;