NM_013363.4:c.865+2887A>C

Variant names:

• chr3-142826805-T-G
• rs2608069
• NM_013363.4:c.865+2887A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013363.4(PCOLCE2):​c.865+2887A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,188 control chromosomes in the GnomAD database, including 609 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 0.074 (609 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013363.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCOLCE2	NM_013363.4	MANE Select	c.865+2887A>C		intron	N/A	NP_037495.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCOLCE2	ENST00000295992.8	TSL:1 MANE Select	c.865+2887A>C		intron	N/A	ENSP00000295992.3
	PCOLCE2	ENST00000964680.1		c.922+2887A>C		intron	N/A	ENSP00000634739.1
	PCOLCE2	ENST00000964678.1		c.865+2887A>C		intron	N/A	ENSP00000634737.1

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11271 AN: 152070 Hom.: 604 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.0543

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0992

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

GnomAD4 genome AF: 0.0741 AC: 11278 AN: 152188 Hom.: 609 Cov.: 32 AF XY: 0.0746 AC XY: 5549 AN XY: 74406

African (AFR) AF: 0.0212 AC: 881 AN: 41536

American (AMR) AF: 0.161 AC: 2455 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3470

East Asian (EAS) AF: 0.170 AC: 876 AN: 5144

South Asian (SAS) AF: 0.0626 AC: 302 AN: 4828

European-Finnish (FIN) AF: 0.0543 AC: 576 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0776 AC: 5277 AN: 68010

Other (OTH) AF: 0.0977 AC: 206 AN: 2108

Alfa AF: 0.0846 Hom.: 1231

Bravo AF: 0.0855

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2608069; hg19: chr3-142545647;