rs1417938
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000567(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 0.254 in 147286 control chromosomes in the gnomAD Genomes database, including 5405 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 ( 5405 hom., cov: 27)
Exomes 𝑓: 0.28 ( 10562 hom. )
Consequence
CRP
NM_000567 intron
NM_000567 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.603
Links
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
?
GnomAd 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 | UniProt |
---|---|---|---|---|---|---|---|
CRP | NM_000567.3 | c.61+29A>T | intron_variant | ENST00000255030.9 | |||
CRP | NM_001329057.2 | c.61+29A>T | intron_variant | ||||
CRP | NM_001329058.2 | c.61+29A>T | intron_variant | ||||
CRP | NM_001382703.1 | c.61+29A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRP | ENST00000255030.9 | c.61+29A>T | intron_variant | 1 | NM_000567.3 | 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 AF XY: 0.295 AC XY: 210864AN XY: 715426
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at