15-49982814-C-T

Variant names:

• chr15-49982814-C-T
• rs8031403
• NM_024837.4:c.749-1520G>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.749-1520G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,976 control chromosomes in the GnomAD database, including 21,668 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 0.51 (21668 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024837.4. 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
	ATP8B4	NM_024837.4	MANE Select	c.749-1520G>A		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.990-1520G>A		intron	N/A
	ATP8B4	NR_073597.2		n.902-1520G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.749-1520G>A		intron	N/A	ENSP00000284509.6	Q8TF62
	ATP8B4	ENST00000557955.5	TSL:1	n.749-1520G>A		intron	N/A	ENSP00000453690.1	H0YMP8
	ATP8B4	ENST00000558906.5	TSL:1	n.*468-1520G>A		intron	N/A	ENSP00000452956.1	H0YLJ1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77574 AN: 151858 Hom.: 21628 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.511 AC: 77689 AN: 151976 Hom.: 21668 Cov.: 32 AF XY: 0.507 AC XY: 37646 AN XY: 74288

African (AFR) AF: 0.734 AC: 30444 AN: 41470

American (AMR) AF: 0.508 AC: 7752 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3462

East Asian (EAS) AF: 0.604 AC: 3115 AN: 5156

South Asian (SAS) AF: 0.560 AC: 2702 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2913 AN: 10568

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27536 AN: 67928

Other (OTH) AF: 0.504 AC: 1062 AN: 2106

Alfa AF: 0.448 Hom.: 20957

Bravo AF: 0.536

Asia WGS AF: 0.622 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.71
PhyloP100		0.18
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: rs8031403; hg19: chr15-50275011;