rs11568663
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005845.5(ABCC4):c.1824+25G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,505,726 control chromosomes in the GnomAD database, including 10,516 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 0.077 ( 630 hom., cov: 32)
Exomes 𝑓: 0.11 ( 9886 hom. )
Consequence
ABCC4
NM_005845.5 intron
NM_005845.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00300
Genes affected
ABCC4 (HGNC:55): (ATP binding cassette subfamily C member 4 (PEL 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 protein is a member of the MRP subfamily which is involved in multi-drug resistance. This family member plays a role in cellular detoxification as a pump for its substrate, organic anions. It may also function in prostaglandin-mediated cAMP signaling in ciliogenesis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2014]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCC4 | NM_005845.5 | c.1824+25G>A | intron_variant | ENST00000645237.2 | NP_005836.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCC4 | ENST00000645237.2 | c.1824+25G>A | intron_variant | NM_005845.5 | ENSP00000494609.1 |
Frequencies
GnomAD3 genomes AF: 0.0772 AC: 11740AN: 152072Hom.: 631 Cov.: 32
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GnomAD3 exomes AF: 0.0806 AC: 18337AN: 227522Hom.: 958 AF XY: 0.0834 AC XY: 10235AN XY: 122692
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GnomAD4 exome AF: 0.114 AC: 154665AN: 1353534Hom.: 9886 Cov.: 19 AF XY: 0.113 AC XY: 76383AN XY: 675312
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GnomAD4 genome AF: 0.0771 AC: 11733AN: 152192Hom.: 630 Cov.: 32 AF XY: 0.0746 AC XY: 5551AN XY: 74426
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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