rs8034382

chr15-49979888-A-G

Variant summary

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

The NM_024837.4(ATP8B4):c.838-75T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,026,604 control chromosomes in the GnomAD database, including 56,236 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 0.40 (13764 hom., cov: 32)
  • Exomes 𝑓: 0.30 (42472 hom.)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

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 (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B4	NM_024837.4	c.838-75T>C		intron_variant		ENST00000284509.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B4	ENST00000284509.11	c.838-75T>C		intron_variant		5	NM_024837.4	P1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60009 AN: 151914 Hom.: 13753 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.328

GnomAD4 exome AF: 0.305 AC: 266461 AN: 874572 Hom.: 42472 AF XY: 0.305 AC XY: 133483 AN XY: 437680

Gnomad4 AFR exome AF: 0.664

Gnomad4 AMR exome AF: 0.302

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.361

Gnomad4 SAS exome AF: 0.314

Gnomad4 FIN exome AF: 0.349

Gnomad4 NFE exome AF: 0.290

Gnomad4 OTH exome AF: 0.302

GnomAD4 genome AF: 0.395 AC: 60071 AN: 152032 Hom.: 13764 Cov.: 32 AF XY: 0.395 AC XY: 29334 AN XY: 74306

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.324

Alfa AF: 0.304 Hom.: 10671

Bravo AF: 0.400

Asia WGS AF: 0.331 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.026
Dann	Benign	0.20

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: rs8034382; hg19: chr15-50272085; COSMIC: COSV52722016; COSMIC: COSV52722016;