rs13089614

Variant names:

• chr3-142825201-G-A
• rs13089614
• NM_013363.4:c.866-1586C>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.866-1586C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 152,050 control chromosomes in the GnomAD database, including 597 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 0.084 (597 hom., cov: 31)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.866-1586C>T		intron_variant	Intron 6 of 8	ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.866-1586C>T		intron_variant	Intron 6 of 8	1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12688 AN: 151932 Hom.: 598 Cov.: 31

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0429

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0835 AC: 12703 AN: 152050 Hom.: 597 Cov.: 31 AF XY: 0.0801 AC XY: 5953 AN XY: 74344

African (AFR) AF: 0.112 AC: 4632 AN: 41456

American (AMR) AF: 0.0668 AC: 1021 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3468

East Asian (EAS) AF: 0.156 AC: 801 AN: 5150

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4814

European-Finnish (FIN) AF: 0.0429 AC: 455 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0758 AC: 5151 AN: 67964

Other (OTH) AF: 0.0773 AC: 163 AN: 2108

Alfa AF: 0.0819 Hom.: 253

Bravo AF: 0.0871

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		0.13
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: rs13089614; hg19: chr3-142544043;