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GeneBe

rs1130864

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000567.3(CRP):c.*224C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 491,546 control chromosomes in the GnomAD database, including 20,033 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 0.26 ( 5728 hom., cov: 32)
Exomes 𝑓: 0.28 ( 14305 hom. )

Consequence

CRP
NM_000567.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61
Variant links:
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CRPNM_000567.3 linkuse as main transcriptc.*224C>T 3_prime_UTR_variant 2/2 ENST00000255030.9
CRPNM_001382703.1 linkuse as main transcriptc.*224C>T 3_prime_UTR_variant 3/3
CRPNM_001329057.2 linkuse as main transcriptc.*22+202C>T intron_variant
CRPNM_001329058.2 linkuse as main transcriptc.*22+202C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRPENST00000255030.9 linkuse as main transcriptc.*224C>T 3_prime_UTR_variant 2/21 NM_000567.3 P1P02741-1

Frequencies

GnomAD3 genomes
AF:
0.261
AC:
39704
AN:
151964
Hom.:
5718
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.156
Gnomad AMI
AF:
0.354
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.306
Gnomad EAS
AF:
0.0603
Gnomad SAS
AF:
0.240
Gnomad FIN
AF:
0.355
Gnomad MID
AF:
0.210
Gnomad NFE
AF:
0.314
Gnomad OTH
AF:
0.270
GnomAD4 exome
AF:
0.279
AC:
94593
AN:
339462
Hom.:
14305
Cov.:
4
AF XY:
0.279
AC XY:
48629
AN XY:
173992
show subpopulations
Gnomad4 AFR exome
AF:
0.153
Gnomad4 AMR exome
AF:
0.338
Gnomad4 ASJ exome
AF:
0.291
Gnomad4 EAS exome
AF:
0.0664
Gnomad4 SAS exome
AF:
0.219
Gnomad4 FIN exome
AF:
0.347
Gnomad4 NFE exome
AF:
0.305
Gnomad4 OTH exome
AF:
0.276
GnomAD4 genome
AF:
0.261
AC:
39754
AN:
152084
Hom.:
5728
Cov.:
32
AF XY:
0.263
AC XY:
19572
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.156
Gnomad4 AMR
AF:
0.308
Gnomad4 ASJ
AF:
0.306
Gnomad4 EAS
AF:
0.0603
Gnomad4 SAS
AF:
0.242
Gnomad4 FIN
AF:
0.355
Gnomad4 NFE
AF:
0.314
Gnomad4 OTH
AF:
0.271
Alfa
AF:
0.303
Hom.:
7135
Bravo
AF:
0.255
Asia WGS
AF:
0.169
AC:
588
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.86
Dann
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1130864; hg19: chr1-159683091; API