rs35604
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000399410.8(ABCC1):c.1678-37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 1,611,314 control chromosomes in the GnomAD database, including 540,370 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 0.83 ( 52447 hom., cov: 32)
Exomes 𝑓: 0.82 ( 487923 hom. )
Consequence
ABCC1
ENST00000399410.8 intron
ENST00000399410.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -6.03
Genes affected
ABCC1 (HGNC:51): (ATP binding cassette subfamily C member 1 (ABCC1 blood group)) 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 full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. This protein functions as a multispecific organic anion transporter, with oxidized glutatione, cysteinyl leukotrienes, and activated aflatoxin B1 as substrates. This protein also transports glucuronides and sulfate conjugates of steroid hormones and bile salts. Alternatively spliced variants of this gene have been described but their full-length nature is unknown. [provided by RefSeq, Apr 2012]
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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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC1 | NM_004996.4 | c.1678-37G>A | intron_variant | ENST00000399410.8 | NP_004987.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC1 | ENST00000399410.8 | c.1678-37G>A | intron_variant | 1 | NM_004996.4 | ENSP00000382342 | P1 |
Frequencies
GnomAD3 genomes AF: 0.829 AC: 126030AN: 152054Hom.: 52411 Cov.: 32
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GnomAD3 exomes AF: 0.791 AC: 195821AN: 247594Hom.: 78261 AF XY: 0.783 AC XY: 105166AN XY: 134374
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GnomAD4 exome AF: 0.816 AC: 1189938AN: 1459142Hom.: 487923 Cov.: 41 AF XY: 0.809 AC XY: 587212AN XY: 725826
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GnomAD4 genome AF: 0.829 AC: 126113AN: 152172Hom.: 52447 Cov.: 32 AF XY: 0.823 AC XY: 61239AN XY: 74394
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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