3-142859962-A-G

Variant summary

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

The NM_013363.4(PCOLCE2):c.193-11490T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,164 control chromosomes in the GnomAD database, including 21,428 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 0.51 (21428 hom., cov: 33)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

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 (NFE) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCOLCE2	NM_013363.4	c.193-11490T>C		intron_variant		ENST00000295992.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.193-11490T>C		intron_variant		1	NM_013363.4	P1
PCOLCE2	ENST00000485766.1	c.193-11490T>C		intron_variant		5
PCOLCE2	ENST00000648195.1	c.193-11490T>C		intron_variant
PCOLCE2	ENST00000495732.5	n.358-11490T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76890 AN: 152046 Hom.: 21423 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.506 AC: 76923 AN: 152164 Hom.: 21428 Cov.: 33 AF XY: 0.503 AC XY: 37453 AN XY: 74392

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.676

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.522

Alfa AF: 0.554 Hom.: 2958

Bravo AF: 0.483

Asia WGS AF: 0.359 AC: 1248 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	0.057
Dann	Benign	0.65

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: rs10935472; hg19: chr3-142578804;