rs10519261

Variant names:

• chr15-50138025-C-G
• rs10519261
• ENST00000895127.1: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.

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000895127.1		c.-42-31017G>C		intron	N/A	ENSP00000565186.1
	ATP8B4	ENST00000966552.1		c.-42-31017G>C		intron	N/A	ENSP00000636611.1
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-31017G>C		intron	N/A	ENSP00000453539.1	H0YMB5

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10519261;

hg19: chr15-50430222;