16-16008018-G-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004996.4(ABCC1):c.225+26G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000381 in 577,684 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000014 ( 0 hom., cov: 29)
Exomes 𝑓: 0.000046 ( 0 hom. )
Consequence
ABCC1
NM_004996.4 intron
NM_004996.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.277
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BS2
High AC in GnomAdExome4 at 20 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000141 AC: 2AN: 141908Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.0000158 AC: 3AN: 189756Hom.: 0 AF XY: 0.0000287 AC XY: 3AN XY: 104644
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GnomAD4 exome AF: 0.0000459 AC: 20AN: 435776Hom.: 0 Cov.: 8 AF XY: 0.0000551 AC XY: 13AN XY: 235750
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GnomAD4 genome AF: 0.0000141 AC: 2AN: 141908Hom.: 0 Cov.: 29 AF XY: 0.0000146 AC XY: 1AN XY: 68684
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at