chr3-142833790-G-T

Variant names:

• chr3-142833790-G-T
• rs6804096
• NM_013363.4:c.711-3944C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013363.4(PCOLCE2):​c.711-3944C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,648 control chromosomes in the GnomAD database, including 11,798 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 0.39 (11798 hom., cov: 31)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.711-3944C>A		intron_variant	Intron 5 of 8	ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.711-3944C>A		intron_variant	Intron 5 of 8	1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58632 AN: 151530 Hom.: 11779 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.387 AC: 58686 AN: 151648 Hom.: 11798 Cov.: 31 AF XY: 0.385 AC XY: 28539 AN XY: 74092

African (AFR) AF: 0.382 AC: 15791 AN: 41334

American (AMR) AF: 0.298 AC: 4534 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1466 AN: 3468

East Asian (EAS) AF: 0.109 AC: 561 AN: 5162

South Asian (SAS) AF: 0.269 AC: 1290 AN: 4788

European-Finnish (FIN) AF: 0.456 AC: 4779 AN: 10488

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28715 AN: 67880

Other (OTH) AF: 0.393 AC: 824 AN: 2098

Alfa AF: 0.261 Hom.: 647

Bravo AF: 0.374

Asia WGS AF: 0.207 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.54
PhyloP100		0.59
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: rs6804096; hg19: chr3-142552632;