chr15-49975700-A-T

Variant names:

• chr15-49975700-A-T
• rs8041517
• NM_024837.4:c.1035-2910T>A

Variant summary

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

The NM_024837.4(ATP8B4):​c.1035-2910T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,968 control chromosomes in the GnomAD database, including 23,762 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 0.53 (23762 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.1035-2910T>A		intron_variant	Intron 12 of 27	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.1035-2910T>A		intron_variant	Intron 12 of 27	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80081 AN: 151852 Hom.: 23704 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.528 AC: 80203 AN: 151968 Hom.: 23762 Cov.: 32 AF XY: 0.523 AC XY: 38863 AN XY: 74260

African (AFR) AF: 0.794 AC: 32941 AN: 41474

American (AMR) AF: 0.539 AC: 8218 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3372 AN: 5172

South Asian (SAS) AF: 0.593 AC: 2859 AN: 4820

European-Finnish (FIN) AF: 0.249 AC: 2625 AN: 10554

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26785 AN: 67906

Other (OTH) AF: 0.539 AC: 1138 AN: 2112

Alfa AF: 0.297 Hom.: 722

Bravo AF: 0.560

Asia WGS AF: 0.663 AC: 2295 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.67
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8041517; hg19: chr15-50267897;