rs35500644
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000567.3(CRP):āc.105T>Gā(p.Thr35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,613,238 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0056 ( 11 hom., cov: 31)
Exomes š: 0.00057 ( 8 hom. )
Consequence
CRP
NM_000567.3 synonymous
NM_000567.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00300
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 1-159714095-A-C is Benign according to our data. Variant chr1-159714095-A-C is described in ClinVar as [Benign]. Clinvar id is 709552.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.003 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00564 (858/152262) while in subpopulation AFR AF= 0.0197 (820/41536). AF 95% confidence interval is 0.0186. There are 11 homozygotes in gnomad4. There are 418 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRP | NM_000567.3 | c.105T>G | p.Thr35= | synonymous_variant | 2/2 | ENST00000255030.9 | |
CRP | NM_001329057.2 | c.105T>G | p.Thr35= | synonymous_variant | 2/3 | ||
CRP | NM_001382703.1 | c.105T>G | p.Thr35= | synonymous_variant | 2/3 | ||
CRP | NM_001329058.2 | c.105T>G | p.Thr35= | synonymous_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRP | ENST00000255030.9 | c.105T>G | p.Thr35= | synonymous_variant | 2/2 | 1 | NM_000567.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00563 AC: 856AN: 152144Hom.: 11 Cov.: 31
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GnomAD3 exomes AF: 0.00137 AC: 339AN: 248090Hom.: 4 AF XY: 0.00111 AC XY: 150AN XY: 134654
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GnomAD4 exome AF: 0.000567 AC: 828AN: 1460976Hom.: 8 Cov.: 31 AF XY: 0.000517 AC XY: 376AN XY: 726880
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GnomAD4 genome ? AF: 0.00564 AC: 858AN: 152262Hom.: 11 Cov.: 31 AF XY: 0.00561 AC XY: 418AN XY: 74474
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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 | Jul 07, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at