1-159714024-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000567.3(CRP):c.176C>T(p.Thr59Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00266 in 1,613,472 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000567.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRP | NM_000567.3 | c.176C>T | p.Thr59Met | missense_variant | Exon 2 of 2 | ENST00000255030.9 | NP_000558.2 | |
CRP | NM_001329057.2 | c.176C>T | p.Thr59Met | missense_variant | Exon 2 of 3 | NP_001315986.1 | ||
CRP | NM_001382703.1 | c.176C>T | p.Thr59Met | missense_variant | Exon 2 of 3 | NP_001369632.1 | ||
CRP | NM_001329058.2 | c.176C>T | p.Thr59Met | missense_variant | Exon 2 of 4 | NP_001315987.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00160 AC: 243AN: 152004Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00145 AC: 363AN: 250722Hom.: 0 AF XY: 0.00142 AC XY: 193AN XY: 135606
GnomAD4 exome AF: 0.00277 AC: 4041AN: 1461350Hom.: 13 Cov.: 31 AF XY: 0.00260 AC XY: 1892AN XY: 727016
GnomAD4 genome AF: 0.00160 AC: 244AN: 152122Hom.: 1 Cov.: 31 AF XY: 0.00129 AC XY: 96AN XY: 74338
ClinVar
Submissions by phenotype
not provided Uncertain:2
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CRP-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at