rs11720678

Variant names:

• chr3-142837004-A-G
• rs11720678
• NM_013363.4:c.710+1766T>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.710+1766T>C 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 152,198 control chromosomes in the GnomAD database, including 2,662 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 (2662 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCOLCE2	NM_013363.4	MANE Select	c.710+1766T>C		intron	N/A	NP_037495.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCOLCE2	ENST00000295992.8	TSL:1 MANE Select	c.710+1766T>C		intron	N/A	ENSP00000295992.3
	PCOLCE2	ENST00000648195.1		c.710+1766T>C		intron	N/A	ENSP00000497763.1
	PCOLCE2	ENST00000485766.1	TSL:5	c.710+1766T>C		intron	N/A	ENSP00000419842.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26422 AN: 152080 Hom.: 2667 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.251

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: 26422 AN: 152198 Hom.: 2662 Cov.: 32 AF XY: 0.174 AC XY: 12937 AN XY: 74402

African (AFR) AF: 0.0766 AC: 3180 AN: 41538

American (AMR) AF: 0.145 AC: 2215 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3472

East Asian (EAS) AF: 0.103 AC: 534 AN: 5180

South Asian (SAS) AF: 0.171 AC: 823 AN: 4826

European-Finnish (FIN) AF: 0.251 AC: 2660 AN: 10578

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15475 AN: 67988

Other (OTH) AF: 0.177 AC: 374 AN: 2114

Alfa AF: 0.201 Hom.: 9061

Bravo AF: 0.161

Asia WGS AF: 0.118 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.69
PhyloP100		0.017
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: rs11720678; hg19: chr3-142555846;