rs9561778
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005845.5(ABCC4):c.3366+1243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 152,000 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 0.0014 ( 0 hom., cov: 31)
Consequence
ABCC4
NM_005845.5 intron
NM_005845.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.10
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC4 | NM_005845.5 | c.3366+1243C>T | intron_variant | ENST00000645237.2 | |||
ABCC4 | NM_001301829.2 | c.3225+1243C>T | intron_variant | ||||
ABCC4 | XM_047430034.1 | c.3237+1243C>T | intron_variant | ||||
ABCC4 | XM_047430035.1 | c.2817+1243C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC4 | ENST00000645237.2 | c.3366+1243C>T | intron_variant | NM_005845.5 | P1 | ||||
ABCC4 | ENST00000646439.1 | c.3225+1243C>T | intron_variant | ||||||
ABCC4 | ENST00000643051.1 | c.*991+1243C>T | intron_variant, NMD_transcript_variant | ||||||
ABCC4 | ENST00000643842.1 | c.*3412+1243C>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00142 AC: 216AN: 151882Hom.: 0 Cov.: 31
GnomAD3 genomes
?
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216
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31
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GnomAD4 genome ? AF: 0.00143 AC: 217AN: 152000Hom.: 0 Cov.: 31 AF XY: 0.00139 AC XY: 103AN XY: 74274
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74274
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ClinVar
Not reported inComputational scores
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Name
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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