rs8039142

Variant names:

• chr15-49980263-C-T
• rs8039142
• NM_024837.4:c.838-450G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024837.4(ATP8B4):​c.838-450G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,018 control chromosomes in the GnomAD database, including 6,389 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 0.28 (6389 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 3 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 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.838-450G>A		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.1079-450G>A		intron	N/A
	ATP8B4	NR_073597.2		n.991-450G>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.838-450G>A		intron	N/A	ENSP00000284509.6	Q8TF62
	ATP8B4	ENST00000557955.5	TSL:1	n.838-450G>A		intron	N/A	ENSP00000453690.1	H0YMP8
	ATP8B4	ENST00000558906.5	TSL:1	n.*557-450G>A		intron	N/A	ENSP00000452956.1	H0YLJ1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41886 AN: 151900 Hom.: 6372 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.276 AC: 41946 AN: 152018 Hom.: 6389 Cov.: 32 AF XY: 0.279 AC XY: 20717 AN XY: 74284

African (AFR) AF: 0.207 AC: 8598 AN: 41474

American (AMR) AF: 0.380 AC: 5795 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1049 AN: 3466

East Asian (EAS) AF: 0.607 AC: 3129 AN: 5154

South Asian (SAS) AF: 0.438 AC: 2107 AN: 4816

European-Finnish (FIN) AF: 0.190 AC: 2007 AN: 10572

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18331 AN: 67962

Other (OTH) AF: 0.307 AC: 649 AN: 2114

Alfa AF: 0.279 Hom.: 20696

Bravo AF: 0.285

Asia WGS AF: 0.540 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	5.9
DANN	Benign	0.76
PhyloP100		0.011
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8039142; hg19: chr15-50272460;