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GeneBe

rs1205

Variant summary

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

The NM_000567.3(CRP):c.*1082G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,742 control chromosomes in the GnomAD database, including 7,941 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.31 ( 7891 hom., cov: 32)
Exomes 𝑓: 0.34 ( 50 hom. )

Consequence

CRP
NM_000567.3 3_prime_UTR

Scores

2

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.313
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 (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CRPNM_000567.3 linkuse as main transcriptc.*1082G>A 3_prime_UTR_variant 2/2 ENST00000255030.9
CRPNM_001329057.2 linkuse as main transcriptc.*374G>A 3_prime_UTR_variant 3/3
CRPNM_001329058.2 linkuse as main transcriptc.*148G>A 3_prime_UTR_variant 4/4
CRPNM_001382703.1 linkuse as main transcriptc.*1082G>A 3_prime_UTR_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRPENST00000255030.9 linkuse as main transcriptc.*1082G>A 3_prime_UTR_variant 2/21 NM_000567.3 P1P02741-1
CRPENST00000437342.1 linkuse as main transcriptc.*374G>A 3_prime_UTR_variant 3/31
CRPENST00000368112.5 linkuse as main transcriptc.*374G>A 3_prime_UTR_variant 4/42 P02741-2
CRPENST00000473196.1 linkuse as main transcriptn.617G>A non_coding_transcript_exon_variant 2/22

Frequencies

GnomAD3 genomes
AF:
0.310
AC:
47083
AN:
151876
Hom.:
7883
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.196
Gnomad AMI
AF:
0.223
Gnomad AMR
AF:
0.372
Gnomad ASJ
AF:
0.361
Gnomad EAS
AF:
0.580
Gnomad SAS
AF:
0.305
Gnomad FIN
AF:
0.371
Gnomad MID
AF:
0.321
Gnomad NFE
AF:
0.334
Gnomad OTH
AF:
0.331
GnomAD4 exome
AF:
0.345
AC:
257
AN:
746
Hom.:
50
Cov.:
0
AF XY:
0.349
AC XY:
145
AN XY:
416
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.250
Gnomad4 ASJ exome
AF:
0.250
Gnomad4 EAS exome
AF:
0.676
Gnomad4 SAS exome
AF:
0.375
Gnomad4 FIN exome
AF:
0.316
Gnomad4 NFE exome
AF:
0.328
Gnomad4 OTH exome
AF:
0.238
GnomAD4 genome
AF:
0.310
AC:
47111
AN:
151996
Hom.:
7891
Cov.:
32
AF XY:
0.314
AC XY:
23355
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.196
Gnomad4 AMR
AF:
0.373
Gnomad4 ASJ
AF:
0.361
Gnomad4 EAS
AF:
0.580
Gnomad4 SAS
AF:
0.305
Gnomad4 FIN
AF:
0.371
Gnomad4 NFE
AF:
0.334
Gnomad4 OTH
AF:
0.330
Alfa
AF:
0.327
Hom.:
9670
Bravo
AF:
0.305
Asia WGS
AF:
0.439
AC:
1527
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Inflammation Uncertain:1
Uncertain significance, no assertion criteria providedreference populationiDNA Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
1.2
Dann
Benign
0.62

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: rs1205; hg19: chr1-159682233; API