rs4762719
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_020297.4(ABCC9):c.1164+23A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00172 in 1,594,076 control chromosomes in the GnomAD database, including 42 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 0.0092 ( 23 hom., cov: 32)
Exomes 𝑓: 0.00093 ( 19 hom. )
Consequence
ABCC9
NM_020297.4 intron
NM_020297.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.221
Genes affected
ABCC9 (HGNC:60): (ATP binding cassette subfamily C member 9) 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 protein is thought to form ATP-sensitive potassium channels in cardiac, skeletal, and vascular and non-vascular smooth muscle. Protein structure suggests a role as the drug-binding channel-modulating subunit of the extra-pancreatic ATP-sensitive potassium channels. Mutations in this gene are associated with cardiomyopathy dilated type 1O. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2011]
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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 (Cadd=2.786).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0092 (1398/152004) while in subpopulation AFR AF= 0.0312 (1294/41502). AF 95% confidence interval is 0.0298. There are 23 homozygotes in gnomad4. There are 663 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 19 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC9 | NM_020297.4 | c.1164+23A>C | intron_variant | ENST00000261200.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC9 | ENST00000261200.9 | c.1164+23A>C | intron_variant | 5 | NM_020297.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00910 AC: 1382AN: 151886Hom.: 19 Cov.: 32
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GnomAD4 exome AF: 0.000933 AC: 1345AN: 1442072Hom.: 19 Cov.: 28 AF XY: 0.000836 AC XY: 601AN XY: 718806
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GnomAD4 genome ? AF: 0.00920 AC: 1398AN: 152004Hom.: 23 Cov.: 32 AF XY: 0.00892 AC XY: 663AN XY: 74328
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ClinVar
Not reported inComputational scores
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Score
Prediction
Cadd
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at