3-142888100-G-C

Position:

• chr3-142888100-G-C

Variant summary

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

The NM_013363.4(PCOLCE2):​c.84-323C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,066 control chromosomes in the GnomAD database, including 7,428 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 0.29 (7428 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCOLCE2	NM_013363.4	c.84-323C>G		intron_variant		ENST00000295992.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.84-323C>G		intron_variant		1	NM_013363.4	P1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43843 AN: 151948 Hom.: 7425 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.273

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.289 AC: 43874 AN: 152066 Hom.: 7428 Cov.: 32 AF XY: 0.286 AC XY: 21231 AN XY: 74334

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.270

Alfa AF: 0.247 Hom.: 687

Bravo AF: 0.305

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.7
DANN	Benign	0.86

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: rs2248811; hg19: chr3-142606942;