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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 0.261 in 151964 control chromosomes in the gnomAD Genomes database, including 5718 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 ( 5718 hom., cov: 32)

Consequence

CRP
NM_000567.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Links

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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
?
GnomAd 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
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
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
0.18
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