15-49964182-G-C

Variant names:

• chr15-49964182-G-C
• rs11070739
• NM_024837.4:c.1244-2162C>G

Variant summary

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

The NM_024837.4(ATP8B4):​c.1244-2162C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,140 control chromosomes in the GnomAD database, including 4,625 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 0.24 (4625 hom., cov: 32)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477

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 = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.1244-2162C>G		intron_variant	Intron 13 of 27	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.1244-2162C>G		intron_variant	Intron 13 of 27	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35738 AN: 152022 Hom.: 4617 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.235 AC: 35789 AN: 152140 Hom.: 4625 Cov.: 32 AF XY: 0.236 AC XY: 17535 AN XY: 74378

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.270

Alfa AF: 0.228 Hom.: 523

Bravo AF: 0.248

Asia WGS AF: 0.387 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.63

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: rs11070739; hg19: chr15-50256379;