15-50061080-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000284509.11(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 ENST00000284509.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000284509.11. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	NM_024837.4	MANE Select	c.87+13047A>C		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.240+13047A>C		intron	N/A
	ATP8B4	NR_073597.2		n.240+13047A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.87+13047A>C		intron	N/A	ENSP00000284509.6
	ATP8B4	ENST00000557955.5	TSL:1	n.87+13047A>C		intron	N/A	ENSP00000453690.1
	ATP8B4	ENST00000558906.5	TSL:1	n.87+13047A>C		intron	N/A	ENSP00000452956.1

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

African (AFR) AF: 0.101 AC: 4196 AN: 41520

American (AMR) AF: 0.189 AC: 2887 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1826 AN: 5174

South Asian (SAS) AF: 0.267 AC: 1288 AN: 4822

European-Finnish (FIN) AF: 0.215 AC: 2278 AN: 10590

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15708 AN: 67936

Other (OTH) AF: 0.208 AC: 440 AN: 2114

Alfa AF: 0.216 Hom.: 11439

Bravo AF: 0.191

Asia WGS AF: 0.266 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.076
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12903325; hg19: chr15-50353277;