Variant chr18-57646551-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001374385.1(ATP8B1):c.*1937T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,620 control chromosomes in the GnomAD database, including 3,915 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3892 hom., cov: 33)

Exomes 𝑓: 0.32 ( 23 hom. )

Consequence

ATP8B1
NM_001374385.1 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.02

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:

(HGNC:):

links:

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

ATP8B1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 18-57646551-A-T is Benign according to our data. Variant chr18-57646551-A-T is described in ClinVar as [Benign]. Clinvar id is 327440.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP8B1	NM_001374385.1 linkuse as main transcript	c.*1937T>A		3_prime_UTR_variant	28/28	ENST00000648908.2	NP_001361314.1
ATP8B1-AS1	NR_164148.1 linkuse as main transcript	n.682+4499A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
ATP8B1	ENST00000648908.2 linkuse as main transcript	c.*1937T>A	3_prime_UTR_variant	28/28		NM_001374385.1	ENSP00000497896	P1
	ENST00000588925.5 linkuse as main transcript	n.570+4499A>T	intron_variant, non_coding_transcript_variant		2
ATP8B1-AS1	ENST00000592201.1 linkuse as main transcript	n.663+4499A>T	intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31190

AN:

152074

Hom.:

3892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0880

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.0160

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.275

Gnomad OTH

AF:

0.233

GnomAD4 exome

AF:

0.320

AC:

137

AN:

428

Hom.:

Cov.:

AF XY:

0.295

AC XY:

AN XY:

258

show subpopulations

Gnomad4 FIN exome

AF:

0.322

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.205

AC:

31197

AN:

152192

Hom.:

3892

Cov.:

AF XY:

0.203

AC XY:

15069

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0880

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.272

Gnomad4 EAS

AF:

0.0160

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.275

Gnomad4 OTH

AF:

0.229

Alfa

AF:

0.238

Hom.:

641

Bravo

AF:

0.190

Asia WGS

AF:

0.112

AC:

389

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Progressive familial intrahepatic cholestasis type 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 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

BayesDel_noAF

Benign

-0.27

CADD

Benign

DANN

Benign

0.86

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