rs3745079

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2

The NM_001374385.1(ATP8B1):​c.234C>G​(p.His78Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,614,062 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0020 ( 11 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 66 hom. )

Consequence

ATP8B1
NM_001374385.1 missense

Scores

18

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -2.14
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

PP2
Missense variant in the ATP8B1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 21 curated pathogenic missense variants (we use a threshold of 10). The gene has 24 curated benign missense variants. Trascript score misZ: 3.3227 (above the threshold of 3.09). GenCC associations: The gene is linked to progressive familial intrahepatic cholestasis type 1, cholestasis, intrahepatic, of pregnancy, 1.
BP4
Computational evidence support a benign effect (MetaRNN=0.0015209615).
BP6
Variant 18-57706535-G-C is Benign according to our data. Variant chr18-57706535-G-C is described in ClinVar as [Benign]. Clinvar id is 259818.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-57706535-G-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00202 (307/152284) while in subpopulation EAS AF= 0.0447 (232/5190). AF 95% confidence interval is 0.04. There are 11 homozygotes in gnomad4. There are 179 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 11 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATP8B1NM_001374385.1 linkc.234C>G p.His78Gln missense_variant Exon 3 of 28 ENST00000648908.2 NP_001361314.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATP8B1ENST00000648908.2 linkc.234C>G p.His78Gln missense_variant Exon 3 of 28 NM_001374385.1 ENSP00000497896.1 O43520

Frequencies

GnomAD3 genomes
AF:
0.00202
AC:
308
AN:
152166
Hom.:
11
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000982
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0448
Gnomad SAS
AF:
0.00809
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00437
AC:
1097
AN:
251254
Hom.:
25
AF XY:
0.00426
AC XY:
578
AN XY:
135814
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.000434
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0471
Gnomad SAS exome
AF:
0.00634
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000704
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00190
AC:
2772
AN:
1461778
Hom.:
66
Cov.:
31
AF XY:
0.00203
AC XY:
1479
AN XY:
727174
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.000403
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0494
Gnomad4 SAS exome
AF:
0.00609
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000989
Gnomad4 OTH exome
AF:
0.00227
GnomAD4 genome
AF:
0.00202
AC:
307
AN:
152284
Hom.:
11
Cov.:
32
AF XY:
0.00240
AC XY:
179
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.000981
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0447
Gnomad4 SAS
AF:
0.00830
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000503
Hom.:
1
Bravo
AF:
0.00187
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00418
AC:
508
Asia WGS
AF:
0.0300
AC:
105
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:4
Jan 06, 2017
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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. -

-
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 08, 2020
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 05, 2015
Eurofins Ntd Llc (ga)
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:3
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Sep 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ATP8B1: BP4, BS1, BS2 -

Jan 01, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Progressive familial intrahepatic cholestasis type 1 Benign:1
Jan 12, 2018
Illumina Laboratory Services, Illumina
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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
0.070
BayesDel_addAF
Benign
-0.63
T
BayesDel_noAF
Benign
-0.63
CADD
Benign
0.0020
DANN
Benign
0.31
DEOGEN2
Benign
0.045
T;T
Eigen
Benign
-2.1
Eigen_PC
Benign
-2.1
FATHMM_MKL
Benign
0.077
N
LIST_S2
Benign
0.47
.;T
MetaRNN
Benign
0.0015
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.94
N;N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-0.060
N;.
REVEL
Benign
0.055
Sift
Benign
0.95
T;.
Sift4G
Benign
0.87
T;.
Polyphen
0.0
B;B
Vest4
0.064
MutPred
0.36
Loss of catalytic residue at M80 (P = 0.0957);Loss of catalytic residue at M80 (P = 0.0957);
MVP
0.35
ClinPred
0.0045
T
GERP RS
-12
Varity_R
0.031
gMVP
0.14

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.

Other links and lift over

dbSNP: rs3745079; hg19: chr18-55373767; COSMIC: COSV52179979; API