15-50141503-T-C

Variant names:

• chr15-50141503-T-C
• rs4774557
• ENST00000558829.1:c.-42-34495A>G

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-42-34495A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,902 control chromosomes in the GnomAD database, including 5,539 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 0.25 (5539 hom., cov: 31)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	XM_011522056.4	c.-42-34495A>G		intron_variant	Intron 1 of 28		XP_011520358.3
ATP8B4	XM_017022587.3	c.-42-34495A>G		intron_variant	Intron 1 of 27		XP_016878076.2
ATP8B4	XM_047433096.1	c.-42-34495A>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.-42-34495A>G		intron_variant	Intron 1 of 3	3		ENSP00000453539.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38685 AN: 151782 Hom.: 5532 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.0915

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.255 AC: 38729 AN: 151902 Hom.: 5539 Cov.: 31 AF XY: 0.262 AC XY: 19427 AN XY: 74254

African (AFR) AF: 0.344 AC: 14246 AN: 41398

American (AMR) AF: 0.267 AC: 4078 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0915 AC: 317 AN: 3466

East Asian (EAS) AF: 0.484 AC: 2491 AN: 5144

South Asian (SAS) AF: 0.349 AC: 1678 AN: 4802

European-Finnish (FIN) AF: 0.255 AC: 2688 AN: 10552

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12476 AN: 67956

Other (OTH) AF: 0.217 AC: 459 AN: 2114

Alfa AF: 0.192 Hom.: 5241

Bravo AF: 0.262

Asia WGS AF: 0.456 AC: 1578 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.26
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs4774557; hg19: chr15-50433700;