rs11853852

Variant names:

• chr15-50119643-C-T
• rs11853852
• XM_011522052.4:c.-354G>A

Variant summary

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

The XM_011522052.4(ATP8B4):​c.-354G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,740 control chromosomes in the GnomAD database, including 17,772 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 0.48 (17772 hom., cov: 30)
• Consequence: ATP8B4 XM_011522052.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-12635G>A		intron	N/A	ENSP00000453539.1
	ATP8B4	ENST00000560437.1	TSL:3	n.-186G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72381 AN: 151624 Hom.: 17757 Cov.: 30

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.477 AC: 72440 AN: 151740 Hom.: 17772 Cov.: 30 AF XY: 0.471 AC XY: 34931 AN XY: 74126

African (AFR) AF: 0.453 AC: 18716 AN: 41324

American (AMR) AF: 0.494 AC: 7521 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2188 AN: 3470

East Asian (EAS) AF: 0.193 AC: 1001 AN: 5176

South Asian (SAS) AF: 0.451 AC: 2171 AN: 4818

European-Finnish (FIN) AF: 0.382 AC: 4004 AN: 10476

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.517 AC: 35152 AN: 67932

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.510 Hom.: 80927

Bravo AF: 0.480

Asia WGS AF: 0.367 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.46
PhyloP100		-0.24
PromoterAI		-0.067	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11853852; hg19: chr15-50411840;