GeneBe

chr3-101575986-C-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020357.3(PCNP):​c.64+1707C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,966 control chromosomes in the GnomAD database, including 4,045 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 0.22 ( 4045 hom., cov: 32)

Consequence

PCNP
NM_020357.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.969

Publications

3 publications found
Variant links:
Genes affected
PCNP (HGNC:30023): (PEST proteolytic signal containing nuclear protein) Involved in proteasome-mediated ubiquitin-dependent protein catabolic process and protein ubiquitination. Located in nuclear body. [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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCNPNM_020357.3 linkc.64+1707C>A intron_variant Intron 1 of 4 ENST00000265260.8 NP_065090.1 Q8WW12-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCNPENST00000265260.8 linkc.64+1707C>A intron_variant Intron 1 of 4 1 NM_020357.3 ENSP00000265260.3 Q8WW12-1

Frequencies

GnomAD3 genomes
AF:
0.223
AC:
33811
AN:
151848
Hom.:
4048
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.159
Gnomad AMI
AF:
0.174
Gnomad AMR
AF:
0.216
Gnomad ASJ
AF:
0.311
Gnomad EAS
AF:
0.286
Gnomad SAS
AF:
0.197
Gnomad FIN
AF:
0.289
Gnomad MID
AF:
0.193
Gnomad NFE
AF:
0.246
Gnomad OTH
AF:
0.218
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.223
AC:
33824
AN:
151966
Hom.:
4045
Cov.:
32
AF XY:
0.225
AC XY:
16707
AN XY:
74260
show subpopulations
African (AFR)
AF:
0.159
AC:
6607
AN:
41460
American (AMR)
AF:
0.215
AC:
3286
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
0.311
AC:
1080
AN:
3468
East Asian (EAS)
AF:
0.286
AC:
1475
AN:
5158
South Asian (SAS)
AF:
0.197
AC:
950
AN:
4816
European-Finnish (FIN)
AF:
0.289
AC:
3043
AN:
10518
Middle Eastern (MID)
AF:
0.194
AC:
57
AN:
294
European-Non Finnish (NFE)
AF:
0.246
AC:
16708
AN:
67974
Other (OTH)
AF:
0.217
AC:
459
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1345
2689
4034
5378
6723
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
362
724
1086
1448
1810
<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:
0.233
Hom.:
2023
Bravo
AF:
0.216
Asia WGS
AF:
0.200
AC:
694
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.4
DANN
Benign
0.34
PhyloP100
-0.97
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: rs17345528; hg19: chr3-101294830; COSMIC: COSV54575578; COSMIC: COSV54575578; API