chr15-50136544-T-C

Variant names:

• chr15-50136544-T-C
• rs17499691
• ENST00000558829.1:c.-42-29536A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000558829.1(ATP8B4):​c.-42-29536A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,268 control chromosomes in the GnomAD database, including 2,255 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 0.16 (2255 hom., cov: 34)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	XM_011522056.4	c.-42-29536A>G		intron_variant	Intron 1 of 28		XP_011520358.3
ATP8B4	XM_017022587.3	c.-42-29536A>G		intron_variant	Intron 1 of 27		XP_016878076.2
ATP8B4	XM_047433096.1	c.-42-29536A>G		intron_variant	Intron 1 of 24		XP_047289052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000558829.1	c.-42-29536A>G		intron_variant	Intron 1 of 3	3		ENSP00000453539.1

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24575 AN: 152150 Hom.: 2252 Cov.: 34

Gnomad AFR AF: 0.0991

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.162 AC: 24596 AN: 152268 Hom.: 2255 Cov.: 34 AF XY: 0.161 AC XY: 12009 AN XY: 74448

African (AFR) AF: 0.0994 AC: 4132 AN: 41556

American (AMR) AF: 0.139 AC: 2131 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.142 AC: 685 AN: 4832

European-Finnish (FIN) AF: 0.213 AC: 2255 AN: 10594

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14049 AN: 68010

Other (OTH) AF: 0.160 AC: 338 AN: 2114

Alfa AF: 0.187 Hom.: 431

Bravo AF: 0.151

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.87
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs17499691; hg19: chr15-50428741;