3-142888100-G-C

Variant summary

Our verdict is Benign. The variant received -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

Publications

1 publications found
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 was made for transcript

Our verdict: Benign. The variant received -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 rank MANE Protein UniProt
PCOLCE2NM_013363.4 linkc.84-323C>G intron_variant Intron 1 of 8 ENST00000295992.8 NP_037495.1 Q9UKZ9
LOC124909443XR_007096122.1 linkn.-164G>C upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCOLCE2ENST00000295992.8 linkc.84-323C>G intron_variant Intron 1 of 8 1 NM_013363.4 ENSP00000295992.3 Q9UKZ9

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
African (AFR)
AF:
0.471
AC:
19530
AN:
41450
American (AMR)
AF:
0.267
AC:
4088
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.247
AC:
858
AN:
3470
East Asian (EAS)
AF:
0.334
AC:
1722
AN:
5154
South Asian (SAS)
AF:
0.245
AC:
1179
AN:
4820
European-Finnish (FIN)
AF:
0.160
AC:
1692
AN:
10586
Middle Eastern (MID)
AF:
0.323
AC:
95
AN:
294
European-Non Finnish (NFE)
AF:
0.205
AC:
13957
AN:
67974
Other (OTH)
AF:
0.270
AC:
569
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1516
3032
4549
6065
7581
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
434
868
1302
1736
2170
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
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
PhyloP100
-1.0
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

Publications

Other links and lift over

dbSNP: rs2248811; hg19: chr3-142606942; API