rs7495057

Variant names:

• chr15-49942966-C-T
• rs7495057
• NM_024837.4:c.1288-8784G>A

Variant summary

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

The NM_024837.4(ATP8B4):​c.1288-8784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,968 control chromosomes in the GnomAD database, including 4,304 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 0.20 (4304 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.1288-8784G>A		intron_variant	Intron 14 of 27	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.1288-8784G>A		intron_variant	Intron 14 of 27	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29584 AN: 151850 Hom.: 4297 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.195 AC: 29635 AN: 151968 Hom.: 4304 Cov.: 32 AF XY: 0.186 AC XY: 13802 AN XY: 74276

African (AFR) AF: 0.411 AC: 17012 AN: 41438

American (AMR) AF: 0.117 AC: 1791 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 383 AN: 3466

East Asian (EAS) AF: 0.0277 AC: 143 AN: 5166

South Asian (SAS) AF: 0.121 AC: 581 AN: 4820

European-Finnish (FIN) AF: 0.0771 AC: 810 AN: 10502

Middle Eastern (MID) AF: 0.152 AC: 44 AN: 290

European-Non Finnish (NFE) AF: 0.124 AC: 8403 AN: 67976

Other (OTH) AF: 0.155 AC: 325 AN: 2102

Alfa AF: 0.137 Hom.: 1850

Bravo AF: 0.205

Asia WGS AF: 0.133 AC: 462 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.41
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7495057; hg19: chr15-50235163;