chr7-87444459-G-T

Variant summary

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

The NM_000443.4(ABCB4):​c.1119+403C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,916 control chromosomes in the GnomAD database, including 37,124 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 0.67 ( 37124 hom., cov: 32)

Consequence

ABCB4
NM_000443.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.706
Variant links:
Genes affected
ABCB4 (HGNC:45): (ATP binding cassette subfamily B member 4) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance as well as antigen presentation. This gene encodes a full transporter and member of the p-glycoprotein family of membrane proteins with phosphatidylcholine as its substrate. The function of this protein has not yet been determined; however, it may involve transport of phospholipids from liver hepatocytes into bile. Alternative splicing of this gene results in several products of undetermined function. [provided by RefSeq, Jul 2008]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ABCB4NM_000443.4 linkuse as main transcriptc.1119+403C>A intron_variant ENST00000649586.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABCB4ENST00000649586.2 linkuse as main transcriptc.1119+403C>A intron_variant NM_000443.4 P1P21439-2

Frequencies

GnomAD3 genomes
AF:
0.675
AC:
102515
AN:
151798
Hom.:
37133
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.390
Gnomad AMI
AF:
0.789
Gnomad AMR
AF:
0.781
Gnomad ASJ
AF:
0.764
Gnomad EAS
AF:
0.609
Gnomad SAS
AF:
0.744
Gnomad FIN
AF:
0.801
Gnomad MID
AF:
0.777
Gnomad NFE
AF:
0.797
Gnomad OTH
AF:
0.725
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.675
AC:
102521
AN:
151916
Hom.:
37124
Cov.:
32
AF XY:
0.677
AC XY:
50248
AN XY:
74232
show subpopulations
Gnomad4 AFR
AF:
0.389
Gnomad4 AMR
AF:
0.781
Gnomad4 ASJ
AF:
0.764
Gnomad4 EAS
AF:
0.610
Gnomad4 SAS
AF:
0.744
Gnomad4 FIN
AF:
0.801
Gnomad4 NFE
AF:
0.797
Gnomad4 OTH
AF:
0.720
Alfa
AF:
0.761
Hom.:
25598
Bravo
AF:
0.659
Asia WGS
AF:
0.677
AC:
2349
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.18
DANN
Benign
0.40

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: rs1149222; hg19: chr7-87073775; COSMIC: COSV55942402; API