chr11-34438994-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001752.4(CAT):c.-20T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 1,575,640 control chromosomes in the GnomAD database, including 329,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.60 ( 28280 hom., cov: 34)
Exomes 𝑓: 0.65 ( 300865 hom. )
Consequence
CAT
NM_001752.4 5_prime_UTR
NM_001752.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.144
Genes affected
CAT (HGNC:1516): (catalase) This gene encodes catalase, a key antioxidant enzyme in the bodies defense against oxidative stress. Catalase is a heme enzyme that is present in the peroxisome of nearly all aerobic cells. Catalase converts the reactive oxygen species hydrogen peroxide to water and oxygen and thereby mitigates the toxic effects of hydrogen peroxide. Oxidative stress is hypothesized to play a role in the development of many chronic or late-onset diseases such as diabetes, asthma, Alzheimer's disease, systemic lupus erythematosus, rheumatoid arthritis, and cancers. Polymorphisms in this gene have been associated with decreases in catalase activity but, to date, acatalasemia is the only disease known to be caused by this gene. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 11-34438994-T-C is Benign according to our data. Variant chr11-34438994-T-C is described in ClinVar as [Benign]. Clinvar id is 559060.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-34438994-T-C is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAT | NM_001752.4 | c.-20T>C | 5_prime_UTR_variant | 1/13 | ENST00000241052.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAT | ENST00000241052.5 | c.-20T>C | 5_prime_UTR_variant | 1/13 | 1 | NM_001752.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.603 AC: 91687AN: 152012Hom.: 28263 Cov.: 34
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GnomAD3 exomes AF: 0.589 AC: 113921AN: 193292Hom.: 34918 AF XY: 0.600 AC XY: 62625AN XY: 104392
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GnomAD4 exome AF: 0.646 AC: 919429AN: 1423512Hom.: 300865 Cov.: 37 AF XY: 0.645 AC XY: 455170AN XY: 705166
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GnomAD4 genome AF: 0.603 AC: 91742AN: 152128Hom.: 28280 Cov.: 34 AF XY: 0.598 AC XY: 44509AN XY: 74376
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 19, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at