rs1205

Variant summary

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

The NM_000567(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 151876 control chromosomes in the gnomAD Genomes database, including 7883 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 ( 7883 hom., cov: 32)

Consequence

CRP
NM_000567 3_prime_UTR

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: -0.313

Links

CRP (HGNC:2367):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
CRP	NM_000567.3 linkuse as main transcript	c.*1082G>A	3_prime_UTR_variant	2/2	ENST00000255030.9
CRP	NM_001329057.2 linkuse as main transcript	c.*374G>A	3_prime_UTR_variant	3/3
CRP	NM_001329058.2 linkuse as main transcript	c.*148G>A	3_prime_UTR_variant	4/4
CRP	NM_001382703.1 linkuse as main transcript	c.*1082G>A	3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRP	ENST00000255030.9 linkuse as main transcript	c.*1082G>A	3_prime_UTR_variant	2/2	1	NM_000567.3	P1	P02741-1
CRP	ENST00000437342.1 linkuse as main transcript	c.*374G>A	3_prime_UTR_variant	3/3	1
CRP	ENST00000368112.5 linkuse as main transcript	c.*374G>A	3_prime_UTR_variant	4/4	2			P02741-2
CRP	ENST00000473196.1 linkuse as main transcript	n.617G>A	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47083

AN:

151876

Hom.:

7883

Cov.:

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.:

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

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 provided

reference population

iDNA Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

Cadd

Benign

1.9

Dann

Benign

0.62

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over