3-142826805-T-G

Variant names:

• chr3-142826805-T-G
• rs2608069
• NM_013363.4:c.865+2887A>C

Variant summary

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

The NM_013363.4(PCOLCE2):​c.865+2887A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,188 control chromosomes in the GnomAD database, including 609 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 0.074 (609 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCOLCE2	NM_013363.4	c.865+2887A>C		intron_variant	Intron 6 of 8	ENST00000295992.8	NP_037495.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.865+2887A>C		intron_variant	Intron 6 of 8	1	NM_013363.4	ENSP00000295992.3

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11271 AN: 152070 Hom.: 604 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0633

Gnomad FIN AF: 0.0543

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.0992

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

GnomAD4 genome AF: 0.0741 AC: 11278 AN: 152188 Hom.: 609 Cov.: 32 AF XY: 0.0746 AC XY: 5549 AN XY: 74406

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.0626

Gnomad4 FIN AF: 0.0543

Gnomad4 NFE AF: 0.0776

Gnomad4 OTH AF: 0.0977

Alfa AF: 0.0837 Hom.: 844

Bravo AF: 0.0855

Asia WGS AF: 0.0890 AC: 309 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	0.89
DANN	Benign	0.75

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: rs2608069; hg19: chr3-142545647;