rs8036777

Variant names:

• chr15-50129221-C-T
• rs8036777
• ENST00000895127.1: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.

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.-42-22213G>A		intron	N/A	ENSP00000565186.1
	ATP8B4	ENST00000966552.1		c.-42-22213G>A		intron	N/A	ENSP00000636611.1
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-22213G>A		intron	N/A	ENSP00000453539.1	H0YMB5

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 v4.9

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;