rs937171

Positions:

• chr15-49902552-C-G

Variant summary

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

The NM_024837.4(ATP8B4):​c.2142-1313G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,058 control chromosomes in the GnomAD database, including 36,058 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 0.68 (36058 hom., cov: 33)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

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]

ATP8B4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.2142-1313G>C		intron_variant		ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.2142-1313G>C		intron_variant		5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103893 AN: 151940 Hom.: 36037 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.684 AC: 103970 AN: 152058 Hom.: 36058 Cov.: 33 AF XY: 0.678 AC XY: 50371 AN XY: 74308

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.659

Alfa AF: 0.684 Hom.: 4466

Bravo AF: 0.684

Asia WGS AF: 0.503 AC: 1752 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.72

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: rs937171; hg19: chr15-50194749;