rs7624656

chr3-142866960-T-C

Variant summary

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

The NM_013363.4(PCOLCE2):c.193-18488A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,156 control chromosomes in the GnomAD database, including 4,828 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 0.19 (4828 hom., cov: 32)
• Consequence: PCOLCE2 NM_013363.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.24

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCOLCE2	NM_013363.4	c.193-18488A>G		intron_variant		ENST00000295992.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCOLCE2	ENST00000295992.8	c.193-18488A>G		intron_variant		1	NM_013363.4	P1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29517 AN: 152038 Hom.: 4799 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.195 AC: 29597 AN: 152156 Hom.: 4828 Cov.: 32 AF XY: 0.189 AC XY: 14052 AN XY: 74408

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0934

Gnomad4 OTH AF: 0.189

Alfa AF: 0.112 Hom.: 1968

Bravo AF: 0.208

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.22
Dann	Benign	0.093

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: rs7624656; hg19: chr3-142585802;