Variant rs2009833 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024837.4(ATP8B4):c.2142-117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,084,428 control chromosomes in the GnomAD database, including 94,047 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 0.40 ( 13255 hom., cov: 33)

Exomes 𝑓: 0.40 ( 80792 hom. )

Consequence

ATP8B4
NM_024837.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.41

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B4	NM_024837.4 linkuse as main transcript	c.2142-117C>T		intron_variant		ENST00000284509.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B4	ENST00000284509.11 linkuse as main transcript	c.2142-117C>T		intron_variant		5	NM_024837.4	P1

Frequencies

GnomAD3 genomes

AF:

0.402

AC:

61141

AN:

151932

Hom.:

13247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.857

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.423

GnomAD4 exome

AF:

0.401

AC:

373874

AN:

932378

Hom.:

80792

AF XY:

0.403

AC XY:

187740

AN XY:

465774

show subpopulations

Gnomad4 AFR exome

AF:

0.310

Gnomad4 AMR exome

AF:

0.578

Gnomad4 ASJ exome

AF:

0.316

Gnomad4 EAS exome

AF:

0.880

Gnomad4 SAS exome

AF:

0.492

Gnomad4 FIN exome

AF:

0.463

Gnomad4 NFE exome

AF:

0.368

Gnomad4 OTH exome

AF:

0.407

GnomAD4 genome

AF:

0.402

AC:

61190

AN:

152050

Hom.:

13255

Cov.:

AF XY:

0.412

AC XY:

30631

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.322

Gnomad4 AMR

AF:

0.526

Gnomad4 ASJ

AF:

0.303

Gnomad4 EAS

AF:

0.857

Gnomad4 SAS

AF:

0.498

Gnomad4 FIN

AF:

0.477

Gnomad4 NFE

AF:

0.376

Gnomad4 OTH

AF:

0.424

Alfa

AF:

0.373

Hom.:

15478

Bravo

AF:

0.400

Asia WGS

AF:

0.649

AC:

2252

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over