rs1417938
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000567.3(CRP):c.61+29A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,583,888 control chromosomes in the GnomAD database, including 70,214 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 0.25 ( 5407 hom., cov: 27)
Exomes 𝑓: 0.30 ( 64807 hom. )
Consequence
CRP
NM_000567.3 intron
NM_000567.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.603
Genes affected
CRP (HGNC:2367): (C-reactive protein) The protein encoded by this gene belongs to the pentraxin family which also includes serum amyloid P component protein and pentraxin 3. Pentraxins are involved in complement activation and amplification via communication with complement initiation pattern recognition molecules, but also complement regulation via recruitment of complement regulators. The encoded protein has a calcium dependent ligand binding domain with a distinctive flattened beta-jellyroll structure. It exists in two forms as either a pentamer in circulation or as a nonsoluble monomer in tissues. It is involved in several host defense related functions based on its ability to recognize foreign pathogens and damaged cells of the host and to initiate their elimination by interacting with humoral and cellular effector systems in the blood. Consequently, the level of this protein in plasma increases greatly during acute phase response to tissue injury, infection, or other inflammatory stimuli. Elevated expression of the encoded protein is associated with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. [provided by RefSeq, Aug 2020]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRP | NM_000567.3 | c.61+29A>T | intron_variant | ENST00000255030.9 | NP_000558.2 | |||
CRP | NM_001329057.2 | c.61+29A>T | intron_variant | NP_001315986.1 | ||||
CRP | NM_001329058.2 | c.61+29A>T | intron_variant | NP_001315987.1 | ||||
CRP | NM_001382703.1 | c.61+29A>T | intron_variant | NP_001369632.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRP | ENST00000255030.9 | c.61+29A>T | intron_variant | 1 | NM_000567.3 | ENSP00000255030 | P1 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 37363AN: 147286Hom.: 5405 Cov.: 27
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GnomAD3 exomes AF: 0.279 AC: 69472AN: 249286Hom.: 10562 AF XY: 0.278 AC XY: 37496AN XY: 134802
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GnomAD4 exome AF: 0.296 AC: 425804AN: 1436510Hom.: 64807 Cov.: 30 AF XY: 0.295 AC XY: 210864AN XY: 715426
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GnomAD4 genome AF: 0.254 AC: 37388AN: 147378Hom.: 5407 Cov.: 27 AF XY: 0.255 AC XY: 18310AN XY: 71718
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at