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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	XM_011522052.4	c.-354G>A		5_prime_UTR_variant	Exon 1 of 29		XP_011520354.1
ATP8B4	XM_011522047.3	c.-43+9G>A		intron_variant	Intron 1 of 28		XP_011520349.1
ATP8B4	XM_011522056.4	c.-42-12635G>A		intron_variant	Intron 1 of 28		XP_011520358.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000558829.1	c.-42-12635G>A		intron_variant	Intron 1 of 3	3		ENSP00000453539.1
ATP8B4	ENST00000560437.1	n.-186G>A		upstream_gene_variant		3

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 v4.3

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;