chr15-50138025-C-G

Position:

• chr15-50138025-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558829.1(ATP8B4):​c.-42-31017G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,170 control chromosomes in the GnomAD database, including 2,247 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 (2247 hom., cov: 32)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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/exons	MANE	UniProt
ATP8B4	XM_011522056.4	c.-42-31017G>C		intron_variant
ATP8B4	XM_017022587.3	c.-42-31017G>C		intron_variant
ATP8B4	XM_047433096.1	c.-42-31017G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B4	ENST00000558829.1	c.-42-31017G>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24544 AN: 152052 Hom.: 2244 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.161 AC: 24565 AN: 152170 Hom.: 2247 Cov.: 32 AF XY: 0.161 AC XY: 11985 AN XY: 74380

Gnomad4 AFR AF: 0.0993

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.161

Alfa AF: 0.187 Hom.: 332

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	-0.82
CADD	Benign	0.66
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519261; hg19: chr15-50430222;