rs1059852

chr15-49859066-G-Achr15-49859066-G-T

Variant summary

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

The NM_024837.4(ATP8B4):c.*1128C>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 0.209 in 151,912 control chromosomes in the GnomAD database, including 3,649 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 0.21 (3649 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ATP8B4 NM_024837.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B4	NM_024837.4	c.*1128C>T		3_prime_UTR_variant	28/28	ENST00000284509.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B4	ENST00000284509.11	c.*1128C>T		3_prime_UTR_variant	28/28	5	NM_024837.4	P1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31707 AN: 151794 Hom.: 3642 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.229

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.209 AC: 31737 AN: 151912 Hom.: 3649 Cov.: 32 AF XY: 0.205 AC XY: 15252 AN XY: 74238

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.0217

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.226

Alfa AF: 0.250 Hom.: 5033

Bravo AF: 0.200

Asia WGS AF: 0.0870 AC: 305 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.65

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: rs1059852; hg19: chr15-50151263;