chr3-142861242-G-C

Variant names:

• chr3-142861242-G-C
• rs920466
• NM_013363.4:c.193-12770C>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.193-12770C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,026 control chromosomes in the GnomAD database, including 25,353 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 0.57 (25353 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 0 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 = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.193-12770C>G		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.193-12770C>G		intron_variant	Intron 2 of 8	1	NM_013363.4	ENSP00000295992.3
PCOLCE2	ENST00000648195.1	c.193-12770C>G		intron_variant	Intron 2 of 8			ENSP00000497763.1
PCOLCE2	ENST00000485766.1	c.193-12770C>G		intron_variant	Intron 2 of 6	5		ENSP00000419842.1
PCOLCE2	ENST00000495732.5	n.358-12770C>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86616 AN: 151908 Hom.: 25324 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.570 AC: 86696 AN: 152026 Hom.: 25353 Cov.: 32 AF XY: 0.566 AC XY: 42050 AN XY: 74334

African (AFR) AF: 0.507 AC: 21030 AN: 41444

American (AMR) AF: 0.499 AC: 7625 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1485 AN: 5164

South Asian (SAS) AF: 0.369 AC: 1780 AN: 4824

European-Finnish (FIN) AF: 0.676 AC: 7147 AN: 10574

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.641 AC: 43545 AN: 67964

Other (OTH) AF: 0.568 AC: 1200 AN: 2114

Alfa AF: 0.483 Hom.: 1391

Bravo AF: 0.555

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.49
PhyloP100		-0.25
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: rs920466; hg19: chr3-142580084;