rs9784320

Variant names:

• chr3-142823192-T-C
• rs9784320
• NM_013363.4:c.949+340A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-142823192-T-C
• chr3-142823192-T-G

Variant summary

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

The NM_013363.4(PCOLCE2):​c.949+340A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,990 control chromosomes in the GnomAD database, including 12,307 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 0.36 (12307 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.949+340A>G		intron_variant	Intron 7 of 8	ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.949+340A>G		intron_variant	Intron 7 of 8	1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54275 AN: 151872 Hom.: 12268 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.358 AC: 54376 AN: 151990 Hom.: 12307 Cov.: 32 AF XY: 0.352 AC XY: 26127 AN XY: 74292

African (AFR) AF: 0.655 AC: 27137 AN: 41408

American (AMR) AF: 0.235 AC: 3579 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 529 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2064 AN: 5172

South Asian (SAS) AF: 0.194 AC: 938 AN: 4826

European-Finnish (FIN) AF: 0.242 AC: 2553 AN: 10570

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16648 AN: 67978

Other (OTH) AF: 0.310 AC: 652 AN: 2106

Alfa AF: 0.256 Hom.: 1183

Bravo AF: 0.373

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.7
DANN	Benign	0.76
PhyloP100		-0.31
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: rs9784320; hg19: chr3-142542034;