rs4148396
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000392.5(ABCC2):c.3258+56T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 1,606,194 control chromosomes in the GnomAD database, including 310,794 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.65 ( 32450 hom., cov: 31)
Exomes 𝑓: 0.62 ( 278344 hom. )
Consequence
ABCC2
NM_000392.5 intron
NM_000392.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.310
Genes affected
ABCC2 (HGNC:53): (ATP binding cassette subfamily C member 2) The 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 MRP subfamily which is involved in multi-drug resistance. This protein is expressed in the canalicular (apical) part of the hepatocyte and functions in biliary transport. Substrates include anticancer drugs such as vinblastine; therefore, this protein appears to contribute to drug resistance in mammalian cells. Several different mutations in this gene have been observed in patients with Dubin-Johnson syndrome (DJS), an autosomal recessive disorder characterized by conjugated hyperbilirubinemia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 10-99832187-T-C is Benign according to our data. Variant chr10-99832187-T-C is described in ClinVar as [Benign]. Clinvar id is 1188977.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC2 | NM_000392.5 | c.3258+56T>C | intron_variant | Intron 23 of 31 | ENST00000647814.1 | NP_000383.2 | ||
ABCC2 | XM_006717630.4 | c.2562+56T>C | intron_variant | Intron 18 of 26 | XP_006717693.1 | |||
ABCC2 | XM_047424598.1 | c.3258+56T>C | intron_variant | Intron 23 of 25 | XP_047280554.1 | |||
ABCC2 | XR_945604.4 | n.3463+56T>C | intron_variant | Intron 23 of 29 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.651 AC: 98805AN: 151874Hom.: 32438 Cov.: 31
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GnomAD4 exome AF: 0.617 AC: 897707AN: 1454202Hom.: 278344 AF XY: 0.617 AC XY: 446840AN XY: 723754
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GnomAD4 genome AF: 0.650 AC: 98863AN: 151992Hom.: 32450 Cov.: 31 AF XY: 0.652 AC XY: 48428AN XY: 74296
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Nov 10, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Dubin-Johnson syndrome Benign:1
Jul 14, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at