rs2248811

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013363.4(PCOLCE2):​c.84-323C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,066 control chromosomes in the GnomAD database, including 7,428 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 0.29 ( 7428 hom., cov: 32)

Consequence

PCOLCE2
NM_013363.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PCOLCE2NM_013363.4 linkuse as main transcriptc.84-323C>G intron_variant ENST00000295992.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PCOLCE2ENST00000295992.8 linkuse as main transcriptc.84-323C>G intron_variant 1 NM_013363.4 P1

Frequencies

GnomAD3 genomes
AF:
0.289
AC:
43843
AN:
151948
Hom.:
7425
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.471
Gnomad AMI
AF:
0.202
Gnomad AMR
AF:
0.267
Gnomad ASJ
AF:
0.247
Gnomad EAS
AF:
0.334
Gnomad SAS
AF:
0.246
Gnomad FIN
AF:
0.160
Gnomad MID
AF:
0.332
Gnomad NFE
AF:
0.205
Gnomad OTH
AF:
0.273
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.289
AC:
43874
AN:
152066
Hom.:
7428
Cov.:
32
AF XY:
0.286
AC XY:
21231
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.471
Gnomad4 AMR
AF:
0.267
Gnomad4 ASJ
AF:
0.247
Gnomad4 EAS
AF:
0.334
Gnomad4 SAS
AF:
0.245
Gnomad4 FIN
AF:
0.160
Gnomad4 NFE
AF:
0.205
Gnomad4 OTH
AF:
0.270
Alfa
AF:
0.247
Hom.:
687
Bravo
AF:
0.305
Asia WGS
AF:
0.303
AC:
1054
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
5.7
DANN
Benign
0.86

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2248811; hg19: chr3-142606942; API