1-159713301-G-A

Position:

• chr1-159713301-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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]

ACMG classification

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	Protein	UniProt
CRP	NM_000567.3	c.*224C>T		3_prime_UTR_variant	2/2	ENST00000255030.9	NP_000558.2
CRP	NM_001382703.1	c.*224C>T		3_prime_UTR_variant	3/3		NP_001369632.1
CRP	NM_001329057.2	c.*22+202C>T		intron_variant			NP_001315986.1
CRP	NM_001329058.2	c.*22+202C>T		intron_variant			NP_001315987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRP	ENST00000255030.9	c.*224C>T		3_prime_UTR_variant	2/2	1	NM_000567.3	ENSP00000255030	P1

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39704 AN: 151964 Hom.: 5718 Cov.: 32

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

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

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

Other links and lift over

dbSNP: rs1130864; hg19: chr1-159683091;