rs10519249

Variant names:

• chr15-49976173-G-A
• rs10519249
• NM_024837.4:c.1035-3383C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-49976173-G-A
• chr15-49976173-G-T

Variant summary

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

The NM_024837.4(ATP8B4):​c.1035-3383C>T 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 151,790 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: 31)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 3 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=-1.0).
• 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.1035-3383C>T		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.1035-3383C>T		intron_variant	Intron 12 of 27	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80089 AN: 151672 Hom.: 23706 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.528 AC: 80209 AN: 151790 Hom.: 23762 Cov.: 31 AF XY: 0.525 AC XY: 38893 AN XY: 74128

African (AFR) AF: 0.794 AC: 32883 AN: 41420

American (AMR) AF: 0.540 AC: 8202 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3464

East Asian (EAS) AF: 0.653 AC: 3367 AN: 5158

South Asian (SAS) AF: 0.595 AC: 2869 AN: 4818

European-Finnish (FIN) AF: 0.259 AC: 2725 AN: 10516

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

European-Non Finnish (NFE) AF: 0.395 AC: 26797 AN: 67904

Other (OTH) AF: 0.541 AC: 1139 AN: 2106

Alfa AF: 0.436 Hom.: 7952

Bravo AF: 0.559

Asia WGS AF: 0.664 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.16
PhyloP100		1.1
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: rs10519249; hg19: chr15-50268370;