chr15-50023056-G-A

Variant names:

• chr15-50023056-G-A
• rs4580097
• NM_024837.4:c.363-12139C>T

Variant summary

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

The NM_024837.4(ATP8B4):​c.363-12139C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,844 control chromosomes in the GnomAD database, including 24,213 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 0.53 (24213 hom., cov: 30)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024837.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	NM_024837.4	MANE Select	c.363-12139C>T		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.516-4080C>T		intron	N/A
	ATP8B4	NR_073597.2		n.516-12139C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.363-12139C>T		intron	N/A	ENSP00000284509.6
	ATP8B4	ENST00000557955.5	TSL:1	n.363-12139C>T		intron	N/A	ENSP00000453690.1
	ATP8B4	ENST00000558906.5	TSL:1	n.363-4080C>T		intron	N/A	ENSP00000452956.1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81083 AN: 151728 Hom.: 24167 Cov.: 30

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.535 AC: 81193 AN: 151844 Hom.: 24213 Cov.: 30 AF XY: 0.537 AC XY: 39806 AN XY: 74190

African (AFR) AF: 0.797 AC: 33038 AN: 41428

American (AMR) AF: 0.541 AC: 8244 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 930 AN: 3462

East Asian (EAS) AF: 0.709 AC: 3652 AN: 5152

South Asian (SAS) AF: 0.564 AC: 2711 AN: 4810

European-Finnish (FIN) AF: 0.410 AC: 4324 AN: 10534

Middle Eastern (MID) AF: 0.348 AC: 101 AN: 290

European-Non Finnish (NFE) AF: 0.394 AC: 26754 AN: 67916

Other (OTH) AF: 0.484 AC: 1015 AN: 2096

Alfa AF: 0.492 Hom.: 2658

Bravo AF: 0.555

Asia WGS AF: 0.672 AC: 2334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.78
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4580097; hg19: chr15-50315253;