rs8036777

Variant names:

• chr15-50129221-C-T
• rs8036777
• ENST00000558829.1:c.-42-22213G>A

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-42-22213G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,856 control chromosomes in the GnomAD database, including 18,871 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 0.48 (18871 hom., cov: 31)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	XM_011522056.4	c.-42-22213G>A		intron_variant	Intron 1 of 28		XP_011520358.3
ATP8B4	XM_017022587.3	c.-42-22213G>A		intron_variant	Intron 1 of 27		XP_016878076.2
ATP8B4	XM_047433096.1	c.-42-22213G>A		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.-42-22213G>A		intron_variant	Intron 1 of 3	3		ENSP00000453539.1

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73083 AN: 151738 Hom.: 18838 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.482 AC: 73166 AN: 151856 Hom.: 18871 Cov.: 31 AF XY: 0.481 AC XY: 35665 AN XY: 74184

African (AFR) AF: 0.665 AC: 27517 AN: 41396

American (AMR) AF: 0.513 AC: 7834 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.546 AC: 2810 AN: 5148

South Asian (SAS) AF: 0.514 AC: 2473 AN: 4808

European-Finnish (FIN) AF: 0.339 AC: 3561 AN: 10514

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26277 AN: 67932

Other (OTH) AF: 0.473 AC: 1001 AN: 2116

Alfa AF: 0.438 Hom.: 8830

Bravo AF: 0.507

Asia WGS AF: 0.584 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.68
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs8036777; hg19: chr15-50421418;