rs2707982

Variant names:

• chr3-142885634-G-A
• rs2707982
• NM_013363.4:c.192+2035C>T

Variant summary

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

The NM_013363.4(PCOLCE2):​c.192+2035C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,958 control chromosomes in the GnomAD database, including 31,836 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 0.64 (31836 hom., cov: 31)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 9 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.192+2035C>T		intron_variant	Intron 2 of 8	ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.192+2035C>T		intron_variant	Intron 2 of 8	1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97862 AN: 151840 Hom.: 31816 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.644 AC: 97925 AN: 151958 Hom.: 31836 Cov.: 31 AF XY: 0.641 AC XY: 47599 AN XY: 74240

African (AFR) AF: 0.721 AC: 29874 AN: 41428

American (AMR) AF: 0.607 AC: 9267 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2243 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2870 AN: 5150

South Asian (SAS) AF: 0.465 AC: 2238 AN: 4816

European-Finnish (FIN) AF: 0.621 AC: 6548 AN: 10550

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42577 AN: 67960

Other (OTH) AF: 0.656 AC: 1382 AN: 2106

Alfa AF: 0.630 Hom.: 41246

Bravo AF: 0.648

Asia WGS AF: 0.521 AC: 1809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.65
PhyloP100		-1.3
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: rs2707982; hg19: chr3-142604476; COSMIC: COSV55998726; COSMIC: COSV55998726;