rs6794287

Variant names:

• chr3-142883824-C-T
• rs6794287
• NM_013363.4:c.192+3845G>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.192+3845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,932 control chromosomes in the GnomAD database, including 5,879 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 0.26 (5879 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.192+3845G>A		intron_variant	Intron 2 of 8	ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.192+3845G>A		intron_variant	Intron 2 of 8	1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38810 AN: 151814 Hom.: 5878 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0752

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.255 AC: 38812 AN: 151932 Hom.: 5879 Cov.: 32 AF XY: 0.254 AC XY: 18880 AN XY: 74248

African (AFR) AF: 0.114 AC: 4714 AN: 41422

American (AMR) AF: 0.231 AC: 3524 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1124 AN: 3462

East Asian (EAS) AF: 0.0750 AC: 388 AN: 5174

South Asian (SAS) AF: 0.122 AC: 587 AN: 4812

European-Finnish (FIN) AF: 0.381 AC: 4008 AN: 10514

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23349 AN: 67962

Other (OTH) AF: 0.261 AC: 551 AN: 2114

Alfa AF: 0.279 Hom.: 1126

Bravo AF: 0.242

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		-0.42
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: rs6794287; hg19: chr3-142602666;