3-142837513-C-T

Variant summary

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

The NM_013363.4(PCOLCE2):c.710+1257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 151,902 control chromosomes in the GnomAD database, including 2,650 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 0.17 (2650 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCOLCE2	NM_013363.4	c.710+1257G>A		intron_variant		ENST00000295992.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.710+1257G>A		intron_variant		1	NM_013363.4	P1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26387 AN: 151784 Hom.: 2655 Cov.: 32

Gnomad AFR AF: 0.0767

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.174 AC: 26387 AN: 151902 Hom.: 2650 Cov.: 32 AF XY: 0.174 AC XY: 12908 AN XY: 74200

Gnomad4 AFR AF: 0.0768

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.177

Alfa AF: 0.197 Hom.: 391

Bravo AF: 0.161

Asia WGS AF: 0.117 AC: 408 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.1
Dann	Benign	0.27

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: rs11712967; hg19: chr3-142556355;