chr16-16033071-T-TCCCTCTTCCTCC
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_004996.4(ABCC1):c.616-36_616-25dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,599,624 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00032 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 2 hom. )
Consequence
ABCC1
NM_004996.4 intron
NM_004996.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.506
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 Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 49 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC1 | NM_004996.4 | c.616-36_616-25dup | intron_variant | ENST00000399410.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC1 | ENST00000399410.8 | c.616-36_616-25dup | intron_variant | 1 | NM_004996.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 152078Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000642 AC: 160AN: 249316Hom.: 1 AF XY: 0.000577 AC XY: 78AN XY: 135272
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GnomAD4 exome AF: 0.000195 AC: 282AN: 1447428Hom.: 2 Cov.: 30 AF XY: 0.000161 AC XY: 116AN XY: 721146
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GnomAD4 genome AF: 0.000322 AC: 49AN: 152196Hom.: 1 Cov.: 32 AF XY: 0.000457 AC XY: 34AN XY: 74416
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at