15-50100798-C-G

Position:

• chr15-50100798-C-G

Variant summary

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

The NM_024837.4(ATP8B4):​c.28+6141G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,042 control chromosomes in the GnomAD database, including 9,163 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 0.33 (9163 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.28+6141G>C		intron_variant		ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.28+6141G>C		intron_variant		5	NM_024837.4	ENSP00000284509	P1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49725 AN: 151924 Hom.: 9141 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.327 AC: 49774 AN: 152042 Hom.: 9163 Cov.: 32 AF XY: 0.334 AC XY: 24861 AN XY: 74352

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.291

Alfa AF: 0.286 Hom.: 836

Bravo AF: 0.337

Asia WGS AF: 0.522 AC: 1810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.53

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: rs7170781; hg19: chr15-50392995;