15-50061080-T-G

Variant names:

• chr15-50061080-T-G
• rs12903325
• NM_024837.4:c.87+13047A>C

Variant summary

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

The NM_024837.4(ATP8B4):​c.87+13047A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,110 control chromosomes in the GnomAD database, including 3,212 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 0.20 (3212 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

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 (EAS) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.87+13047A>C		intron_variant	Intron 3 of 27	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.87+13047A>C		intron_variant	Intron 3 of 27	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29881 AN: 151992 Hom.: 3210 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.197 AC: 29892 AN: 152110 Hom.: 3212 Cov.: 32 AF XY: 0.197 AC XY: 14674 AN XY: 74382

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.208

Alfa AF: 0.222 Hom.: 7800

Bravo AF: 0.191

Asia WGS AF: 0.266 AC: 929 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	1.7
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12903325; hg19: chr15-50353277;