rs35677492
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001752.4(CAT):c.1560G>A(p.Ala520=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000257 in 1,613,812 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00029 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00025 ( 1 hom. )
Consequence
CAT
NM_001752.4 synonymous
NM_001752.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.385
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 11-34471409-G-A is Benign according to our data. Variant chr11-34471409-G-A is described in ClinVar as [Benign]. Clinvar id is 781676.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.385 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAT | NM_001752.4 | c.1560G>A | p.Ala520= | synonymous_variant | 13/13 | ENST00000241052.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAT | ENST00000241052.5 | c.1560G>A | p.Ala520= | synonymous_variant | 13/13 | 1 | NM_001752.4 | P1 | |
CAT | ENST00000534710.2 | n.370G>A | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152182Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000502 AC: 126AN: 251110Hom.: 0 AF XY: 0.000516 AC XY: 70AN XY: 135724
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GnomAD4 exome AF: 0.000253 AC: 370AN: 1461630Hom.: 1 Cov.: 30 AF XY: 0.000261 AC XY: 190AN XY: 727124
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GnomAD4 genome ? AF: 0.000289 AC: 44AN: 152182Hom.: 1 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74336
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
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