rs6794287

chr3-142883824-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.192+3845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,932 control chromosomes in the GnomAD database, including 5,879 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 (5879 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCOLCE2	NM_013363.4	c.192+3845G>A		intron_variant		ENST00000295992.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.192+3845G>A		intron_variant		1	NM_013363.4	P1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38810 AN: 151814 Hom.: 5878 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0752

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.255 AC: 38812 AN: 151932 Hom.: 5879 Cov.: 32 AF XY: 0.254 AC XY: 18880 AN XY: 74248

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0750

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.261

Alfa AF: 0.284 Hom.: 1123

Bravo AF: 0.242

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.1
Dann	Benign	0.80

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: rs6794287; hg19: chr3-142602666;