ENST00000558829.1:c.-42-31017G>C

Variant names:

• chr15-50138025-C-G
• rs10519261
• ENST00000558829.1:c.-42-31017G>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.82).
• 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 rank	MANE	Protein	UniProt
ATP8B4	XM_011522056.4	c.-42-31017G>C		intron_variant	Intron 1 of 28		XP_011520358.3
ATP8B4	XM_017022587.3	c.-42-31017G>C		intron_variant	Intron 1 of 27		XP_016878076.2
ATP8B4	XM_047433096.1	c.-42-31017G>C		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.-42-31017G>C		intron_variant	Intron 1 of 3	3		ENSP00000453539.1

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

African (AFR) AF: 0.0993 AC: 4122 AN: 41520

American (AMR) AF: 0.139 AC: 2130 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5186

South Asian (SAS) AF: 0.141 AC: 682 AN: 4826

European-Finnish (FIN) AF: 0.212 AC: 2247 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14038 AN: 67984

Other (OTH) AF: 0.161 AC: 340 AN: 2116

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10519261; hg19: chr15-50430222;