rs7624656

Variant names:

• chr3-142866960-T-C
• rs7624656
• NM_013363.4:c.193-18488A>G

Variant summary

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

The NM_013363.4(PCOLCE2):​c.193-18488A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,156 control chromosomes in the GnomAD database, including 4,828 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 0.19 (4828 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.446 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.193-18488A>G		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.193-18488A>G		intron	N/A	ENSP00000295992.3
	PCOLCE2	ENST00000648195.1		c.193-18488A>G		intron	N/A	ENSP00000497763.1
	PCOLCE2	ENST00000485766.1	TSL:5	c.193-18488A>G		intron	N/A	ENSP00000419842.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29517 AN: 152038 Hom.: 4799 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.195 AC: 29597 AN: 152156 Hom.: 4828 Cov.: 32 AF XY: 0.189 AC XY: 14052 AN XY: 74408

African (AFR) AF: 0.451 AC: 18708 AN: 41448

American (AMR) AF: 0.129 AC: 1970 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.0602 AC: 312 AN: 5184

South Asian (SAS) AF: 0.121 AC: 583 AN: 4826

European-Finnish (FIN) AF: 0.0718 AC: 762 AN: 10612

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0934 AC: 6355 AN: 68010

Other (OTH) AF: 0.189 AC: 400 AN: 2114

Alfa AF: 0.143 Hom.: 5173

Bravo AF: 0.208

Asia WGS AF: 0.111 AC: 386 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	0.22
DANN	Benign	0.093
PhyloP100		-3.2
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: rs7624656; hg19: chr3-142585802;