10-99844024-C-G
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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.3843+124C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 913,174 control chromosomes in the GnomAD database, including 55,169 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.31 ( 7705 hom., cov: 32)
Exomes 𝑓: 0.35 ( 47464 hom. )
Consequence
ABCC2
NM_000392.5 intron
NM_000392.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.585
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=-0.9).
BP6
Variant 10-99844024-C-G is Benign according to our data. Variant chr10-99844024-C-G is described in ClinVar as [Benign]. Clinvar id is 1275707.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC2 | NM_000392.5 | c.3843+124C>G | intron_variant | ENST00000647814.1 | NP_000383.2 | |||
ABCC2 | XM_006717630.4 | c.3147+124C>G | intron_variant | XP_006717693.1 | ||||
ABCC2 | XR_945604.4 | n.4048+124C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC2 | ENST00000647814.1 | c.3843+124C>G | intron_variant | NM_000392.5 | ENSP00000497274.1 | |||||
ABCC2 | ENST00000649459.1 | n.191+124C>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.306 AC: 46486AN: 151976Hom.: 7710 Cov.: 32
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GnomAD4 exome AF: 0.350 AC: 266338AN: 761078Hom.: 47464 AF XY: 0.350 AC XY: 141379AN XY: 403498
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GnomAD4 genome AF: 0.306 AC: 46498AN: 152096Hom.: 7705 Cov.: 32 AF XY: 0.306 AC XY: 22715AN XY: 74330
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at