rs12968116

Positions:

chr18-57655270-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1

The NM_001374385.1(ATP8B1):c.2855G>A(p.Arg952Gln) variant causes a missense change. The variant allele was found at a frequency of 0.105 in 1,613,884 control chromosomes in the GnomAD database, including 9,838 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.079 ( 644 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9194 hom. )

Consequence

ATP8B1
NM_001374385.1 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 5.05

Variant links:

Genes affected

ATP8B1 (HGNC:3706): (ATPase phospholipid transporting 8B1) This gene encodes a member of the P-type cation transport ATPase family, which belongs to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. Mutations in this gene may result in progressive familial intrahepatic cholestasis type 1 and in benign recurrent intrahepatic cholestasis. [provided by RefSeq, Jul 2008]

ATP8B1 links:

ATP8B1-AS1 (HGNC:56042): (ATP8B1 antisense RNA 1)

ATP8B1-AS1 links:

ENSG00000267787 (HGNC:):

ENSG00000267787 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

PP2

Missense variant in gene, where missense usually causes diseases (based on misZ statistic), ATP8B1. . Trascript score misZ: 3.3227 (greater than threshold 3.09). The gene has 21 curated pathogenic missense variants (we use a threshold of 10). The gene has 24 curated benign missense variants. GenCC has associacion of the gene with progressive familial intrahepatic cholestasis type 1, cholestasis, intrahepatic, of pregnancy, 1.

BP4

Computational evidence support a benign effect (MetaRNN=0.0027029812).

BP6

Variant 18-57655270-C-T is Benign according to our data. Variant chr18-57655270-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 259820.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-57655270-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP8B1	NM_001374385.1 link	c.2855G>A	p.Arg952Gln	missense_variant	23/28	ENST00000648908.2	NP_001361314.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP8B1	ENST00000648908.2 link	c.2855G>A	p.Arg952Gln	missense_variant	23/28		NM_001374385.1	ENSP00000497896.1		O43520

Frequencies

GnomAD3 genomes

AF:

0.0794

AC:

12075

AN:

152112

Hom.:

643

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0278

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.0653

Gnomad ASJ

AF:

0.0857

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0536

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.0803

GnomAD3 exomes

AF:

0.0824

AC:

20731

AN:

251472

Hom.:

1082

AF XY:

0.0839

AC XY:

11401

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.0247

Gnomad AMR exome

AF:

0.0408

Gnomad ASJ exome

AF:

0.0821

Gnomad EAS exome

AF:

0.000489

Gnomad SAS exome

AF:

0.0469

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.0858

GnomAD4 exome

AF:

0.108

AC:

157146

AN:

1461654

Hom.:

9194

Cov.:

AF XY:

0.106

AC XY:

77069

AN XY:

727152

show subpopulations

Gnomad4 AFR exome

AF:

0.0247

Gnomad4 AMR exome

AF:

0.0435

Gnomad4 ASJ exome

AF:

0.0846

Gnomad4 EAS exome

AF:

0.000378

Gnomad4 SAS exome

AF:

0.0501

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.122

Gnomad4 OTH exome

AF:

0.0985

GnomAD4 genome

AF:

0.0793

AC:

12073

AN:

152230

Hom.:

644

Cov.:

AF XY:

0.0783

AC XY:

5827

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0278

Gnomad4 AMR

AF:

0.0652

Gnomad4 ASJ

AF:

0.0857

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0535

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.0795

Alfa

AF:

0.105

Hom.:

2212

Bravo

AF:

0.0748

TwinsUK

AF:

0.118

AC:

439

ALSPAC

AF:

0.122

AC:

472

ESP6500AA

AF:

0.0250

AC:

110

ESP6500EA

AF:

0.115

AC:

987

ExAC

AF:

0.0854

AC:

10375

Asia WGS

AF:

0.0300

AC:

105

AN:

3478

EpiCase

AF:

0.110

EpiControl

AF:

0.109

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:6

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 23, 2015	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 03, 2021	- -

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Progressive familial intrahepatic cholestasis type 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.28

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.22

T;T

Eigen

Uncertain

0.54

Eigen_PC

Uncertain

0.60

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.88

.;D

MetaRNN

Benign

0.0027

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.12

N;N

PrimateAI

Pathogenic

0.81

PROVEAN

Benign

-1.7

N;.

REVEL

Uncertain

0.37

Sift

Benign

0.28

T;.

Sift4G

Benign

0.18

T;.

Polyphen

1.0

D;D

Vest4

0.17

ClinPred

0.011

GERP RS

5.9

Varity_R

0.37

gMVP

0.68

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over