chr11-34453840-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001752.4(CAT):c.625C>T(p.His209Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,613,330 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001752.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAT | NM_001752.4 | c.625C>T | p.His209Tyr | missense_variant | 6/13 | ENST00000241052.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAT | ENST00000241052.5 | c.625C>T | p.His209Tyr | missense_variant | 6/13 | 1 | NM_001752.4 | P1 | |
CAT | ENST00000650153.1 | c.*445C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/9 | |||||
CAT | ENST00000528104.2 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00152 AC: 231AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00184 AC: 463AN: 251468Hom.: 0 AF XY: 0.00194 AC XY: 264AN XY: 135910
GnomAD4 exome AF: 0.00205 AC: 2995AN: 1461008Hom.: 3 Cov.: 30 AF XY: 0.00203 AC XY: 1477AN XY: 726882
GnomAD4 genome AF: 0.00152 AC: 231AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.00157 AC XY: 117AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Nov 07, 2023 | Variant summary: CAT c.625C>T (p.His209Tyr) results in a conservative amino acid change located in the Catalase core domain (IPR011614) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.002 in 1613330 control chromosomes, predominantly at a frequency of 0.0023 within the Non-Finnish European subpopulation in the gnomAD database, including 3 homozygotes suggesting a benign role. To our knowledge, no occurrence of c.625C>T in individuals affected with Acatalasia and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at