15-50137031-C-G

Variant names:

• chr15-50137031-C-G
• rs17499726
• ENST00000895127.1:c.-42-30023G>C

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-42-30023G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0942 in 152,184 control chromosomes in the GnomAD database, including 863 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 0.094 (863 hom., cov: 32)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 2 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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.-42-30023G>C		intron	N/A	ENSP00000565186.1
	ATP8B4	ENST00000966552.1		c.-42-30023G>C		intron	N/A	ENSP00000636611.1
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-30023G>C		intron	N/A	ENSP00000453539.1	H0YMB5

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14334 AN: 152066 Hom.: 864 Cov.: 32

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0942 AC: 14335 AN: 152184 Hom.: 863 Cov.: 32 AF XY: 0.0966 AC XY: 7189 AN XY: 74402

African (AFR) AF: 0.0305 AC: 1268 AN: 41530

American (AMR) AF: 0.107 AC: 1635 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3472

East Asian (EAS) AF: 0.0336 AC: 174 AN: 5186

South Asian (SAS) AF: 0.0586 AC: 283 AN: 4830

European-Finnish (FIN) AF: 0.174 AC: 1836 AN: 10566

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8353 AN: 67994

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.107 Hom.: 130

Bravo AF: 0.0846

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	17
DANN	Benign	0.84
PhyloP100		1.3

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: rs17499726;

hg19: chr15-50429228;