3-142816567-C-G

Position:

• chr3-142816567-C-G

Variant summary

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

The ENST00000470310.5(PCOLCE2):​n.*193G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,142 control chromosomes in the GnomAD database, including 10,631 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 0.33 (10630 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1 hom.)
• Consequence: PCOLCE2 ENST00000470310.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.755

Genes affected

PCOLCE2 (HGNC:8739): (procollagen C-endopeptidase enhancer 2) Enables collagen binding activity; heparin binding activity; and peptidase activator activity. Predicted to be involved in positive regulation of peptidase activity. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.142816567C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000470310.5	n.*193G>C		non_coding_transcript_exon_variant	5/6	5		ENSP00000419643.1
PCOLCE2	ENST00000470310.5	n.*193G>C		3_prime_UTR_variant	5/6	5		ENSP00000419643.1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50515 AN: 151982 Hom.: 10587 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.289

GnomAD4 exome AF: 0.250 AC: 10 AN: 40 Hom.: 1 Cov.: 0 AF XY: 0.269 AC XY: 7 AN XY: 26

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.267

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.333 AC: 50625 AN: 152102 Hom.: 10630 Cov.: 32 AF XY: 0.326 AC XY: 24259 AN XY: 74388

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.297

Alfa AF: 0.286 Hom.: 1005

Bravo AF: 0.347

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1871349; hg19: chr3-142535409;