rs12309211
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020898.3(CALCOCO1):c.*1696C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,006 control chromosomes in the GnomAD database, including 24,463 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 0.57 ( 24450 hom., cov: 31)
Exomes 𝑓: 0.58 ( 13 hom. )
Consequence
CALCOCO1
NM_020898.3 3_prime_UTR
NM_020898.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.05
Genes affected
CALCOCO1 (HGNC:29306): (calcium binding and coiled-coil domain 1) Enables several functions, including armadillo repeat domain binding activity; beta-catenin binding activity; and nuclear receptor coactivator activity. Involved in positive regulation of gene expression and positive regulation of transcription, DNA-templated. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.5).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CALCOCO1 | NM_020898.3 | c.*1696C>T | 3_prime_UTR_variant | 15/15 | ENST00000550804.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CALCOCO1 | ENST00000550804.6 | c.*1696C>T | 3_prime_UTR_variant | 15/15 | 1 | NM_020898.3 | P4 | ||
CALCOCO1 | ENST00000262059.8 | c.*1696C>T | 3_prime_UTR_variant | 15/15 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.565 AC: 85808AN: 151810Hom.: 24414 Cov.: 31
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GnomAD4 exome AF: 0.577 AC: 45AN: 78Hom.: 13 Cov.: 0 AF XY: 0.571 AC XY: 24AN XY: 42
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GnomAD4 genome ? AF: 0.565 AC: 85892AN: 151928Hom.: 24450 Cov.: 31 AF XY: 0.563 AC XY: 41777AN XY: 74248
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at