rs10519262

Variant names:

• chr15-50140297-G-A
• rs10519262
• ENST00000558829.1: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	XM_011522056.4	c.-42-33289C>T		intron_variant	Intron 1 of 28		XP_011520358.3
ATP8B4	XM_017022587.3	c.-42-33289C>T		intron_variant	Intron 1 of 27		XP_016878076.2
ATP8B4	XM_047433096.1	c.-42-33289C>T		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.-42-33289C>T		intron_variant	Intron 1 of 3	3		ENSP00000453539.1

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 v4.3

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

Other links and lift over

dbSNP: rs10519262; hg19: chr15-50432494;