chr3-142820647-C-T

Variant names:

• chr3-142820647-C-T
• rs13060227
• NM_013363.4:c.1117+231G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_013363.4(PCOLCE2):​c.1117+231G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 152,260 control chromosomes in the GnomAD database, including 88 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 0.032 (88 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• 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=-0.89).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.032 (4877/152260) while in subpopulation EAS AF = 0.055 (285/5186). AF 95% confidence interval is 0.0497. There are 88 homozygotes in GnomAd4. There are 2284 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 88 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.1117+231G>A		intron_variant	Intron 8 of 8	ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.1117+231G>A		intron_variant	Intron 8 of 8	1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4869 AN: 152142 Hom.: 88 Cov.: 32

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0320 AC: 4877 AN: 152260 Hom.: 88 Cov.: 32 AF XY: 0.0307 AC XY: 2284 AN XY: 74454

African (AFR) AF: 0.0346 AC: 1439 AN: 41552

American (AMR) AF: 0.0247 AC: 377 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3470

East Asian (EAS) AF: 0.0550 AC: 285 AN: 5186

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4824

European-Finnish (FIN) AF: 0.0219 AC: 232 AN: 10604

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2364 AN: 68014

Other (OTH) AF: 0.0312 AC: 66 AN: 2114

Alfa AF: 0.0334 Hom.: 73

Bravo AF: 0.0320

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.36
PhyloP100		-0.82
Mutation Taster		=100/0	polymorphism

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: rs13060227; hg19: chr3-142539489;