rs10519262

Variant names:

• chr15-50140297-G-A
• rs10519262
• ENST00000895127.1:c.-42-33289C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-50140297-G-A
• chr15-50140297-G-T

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-42-33289C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,118 control chromosomes in the GnomAD database, including 4,499 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 0.22 (4499 hom., cov: 32)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 16 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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.-42-33289C>T		intron	N/A	ENSP00000565186.1
	ATP8B4	ENST00000966552.1		c.-42-33289C>T		intron	N/A	ENSP00000636611.1
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-33289C>T		intron	N/A	ENSP00000453539.1	H0YMB5

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34050 AN: 152000 Hom.: 4499 Cov.: 32

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.224 AC: 34041 AN: 152118 Hom.: 4499 Cov.: 32 AF XY: 0.224 AC XY: 16655 AN XY: 74362

African (AFR) AF: 0.0754 AC: 3132 AN: 41524

American (AMR) AF: 0.226 AC: 3454 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1091 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2160 AN: 5164

South Asian (SAS) AF: 0.284 AC: 1372 AN: 4824

European-Finnish (FIN) AF: 0.265 AC: 2796 AN: 10556

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19204 AN: 67992

Other (OTH) AF: 0.245 AC: 517 AN: 2112

Alfa AF: 0.258 Hom.: 6868

Bravo AF: 0.214

Asia WGS AF: 0.287 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.69
PhyloP100		-0.31

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: rs10519262;

hg19: chr15-50432494;