rs7639314

chr3-142884268-G-Achr3-142884268-G-T

Variant summary

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

The NM_013363.4(PCOLCE2):c.192+3401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,004 control chromosomes in the GnomAD database, including 3,321 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 0.20 (3321 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCOLCE2	NM_013363.4	c.192+3401C>T		intron_variant		ENST00000295992.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.192+3401C>T		intron_variant		1	NM_013363.4	P1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30217 AN: 151886 Hom.: 3324 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.199 AC: 30226 AN: 152004 Hom.: 3321 Cov.: 32 AF XY: 0.204 AC XY: 15171 AN XY: 74266

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.211

Alfa AF: 0.220 Hom.: 7753

Bravo AF: 0.184

Asia WGS AF: 0.222 AC: 771 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	0.45
Dann	Benign	0.48

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: rs7639314; hg19: chr3-142603110;