rs4494483

Positions:

• chr15-49860077-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024837.4(ATP8B4):​c.*117A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,285,546 control chromosomes in the GnomAD database, including 46,394 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 0.26 (5172 hom., cov: 32)
  • Exomes 𝑓: 0.26 (41222 hom.)
• Consequence: ATP8B4 NM_024837.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.*117A>T		3_prime_UTR_variant	28/28	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509	c.*117A>T		3_prime_UTR_variant	28/28	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38777 AN: 151984 Hom.: 5163 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.263 AC: 298421 AN: 1133444 Hom.: 41222 Cov.: 16 AF XY: 0.263 AC XY: 148774 AN XY: 565446

Gnomad4 AFR exome AF: 0.262

Gnomad4 AMR exome AF: 0.155

Gnomad4 ASJ exome AF: 0.246

Gnomad4 EAS exome AF: 0.0224

Gnomad4 SAS exome AF: 0.238

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.279

Gnomad4 OTH exome AF: 0.260

GnomAD4 genome AF: 0.255 AC: 38811 AN: 152102 Hom.: 5172 Cov.: 32 AF XY: 0.250 AC XY: 18618 AN XY: 74362

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.256

Alfa AF: 0.264 Hom.: 695

Bravo AF: 0.249

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.075
DANN	Benign	0.82

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

Publications

LitVar

Other links and lift over

dbSNP: rs4494483; hg19: chr15-50152274;