3-142828420-T-C

Position:

• chr3-142828420-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013363.4(PCOLCE2):​c.865+1272A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,134 control chromosomes in the GnomAD database, including 3,948 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 0.21 (3948 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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]

PCOLCE2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.865+1272A>G		intron_variant		ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.865+1272A>G		intron_variant		1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31971 AN: 152016 Hom.: 3949 Cov.: 32

Gnomad AFR AF: 0.0841

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.210 AC: 31972 AN: 152134 Hom.: 3948 Cov.: 32 AF XY: 0.210 AC XY: 15606 AN XY: 74372

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.207

Alfa AF: 0.256 Hom.: 2458

Bravo AF: 0.197

Asia WGS AF: 0.138 AC: 481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs11712986; hg19: chr3-142547262;