rs1059850

chr15-49859332-G-A

Variant summary

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

The NM_024837.4(ATP8B4):c.*862C>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 0.292 in 152,052 control chromosomes in the GnomAD database, including 6,845 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 0.29 (6845 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ATP8B4 NM_024837.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B4	NM_024837.4	c.*862C>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.*862C>T		3_prime_UTR_variant	28/28	5	NM_024837.4	P1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44308 AN: 151934 Hom.: 6833 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.286

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: 0.292 AC: 44362 AN: 152052 Hom.: 6845 Cov.: 32 AF XY: 0.286 AC XY: 21291 AN XY: 74336

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.0316

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.284

Alfa AF: 0.297 Hom.: 1098

Bravo AF: 0.286

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.19
Dann	Benign	0.71

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: rs1059850; hg19: chr15-50151529;