chr1-186312564-T-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003292.3(TPR):c.*1407A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 787,338 control chromosomes in the GnomAD database, including 162,257 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 0.63 ( 30693 hom., cov: 32)
Exomes 𝑓: 0.64 ( 131564 hom. )
Consequence
TPR
NM_003292.3 3_prime_UTR
NM_003292.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.405
Publications
8 publications found
Genes affected
TPR (HGNC:12017): (translocated promoter region, nuclear basket protein) This gene encodes a large coiled-coil protein that forms intranuclear filaments attached to the inner surface of nuclear pore complexes (NPCs). The protein directly interacts with several components of the NPC. It is required for the nuclear export of mRNAs and some proteins. Oncogenic fusions of the 5' end of this gene with several different kinase genes occur in some neoplasias. [provided by RefSeq, Jul 2008]
PRG4 (HGNC:9364): (proteoglycan 4) The protein encoded by this gene is a large proteoglycan that is synthesized by chondrocytes located at the surface of articular cartilage and by some synovial lining cells. This protein contains both chondroitin sulfate and keratan sulfate glycosaminoglycans. It functions as a boundary lubricant at the cartilage surface and contributes to the elastic absorption and energy dissipation of synovial fluid. Mutations in this gene result in camptodactyly-arthropathy-coxa vara-pericarditis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
PRG4 Gene-Disease associations (from GenCC):
- camptodactyly-arthropathy-coxa vara-pericarditis syndromeInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Illumina, ClinGen
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.635 AC: 96367AN: 151854Hom.: 30638 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
96367
AN:
151854
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.641 AC: 407486AN: 635364Hom.: 131564 Cov.: 8 AF XY: 0.637 AC XY: 208806AN XY: 327770 show subpopulations
GnomAD4 exome
AF:
AC:
407486
AN:
635364
Hom.:
Cov.:
8
AF XY:
AC XY:
208806
AN XY:
327770
show subpopulations
African (AFR)
AF:
AC:
9840
AN:
15586
American (AMR)
AF:
AC:
11728
AN:
19730
Ashkenazi Jewish (ASJ)
AF:
AC:
8239
AN:
15058
East Asian (EAS)
AF:
AC:
21603
AN:
32222
South Asian (SAS)
AF:
AC:
26964
AN:
49076
European-Finnish (FIN)
AF:
AC:
20727
AN:
31834
Middle Eastern (MID)
AF:
AC:
1220
AN:
2368
European-Non Finnish (NFE)
AF:
AC:
287042
AN:
437308
Other (OTH)
AF:
AC:
20123
AN:
32182
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
7437
14874
22310
29747
37184
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.635 AC: 96475AN: 151974Hom.: 30693 Cov.: 32 AF XY: 0.634 AC XY: 47076AN XY: 74276 show subpopulations
GnomAD4 genome
AF:
AC:
96475
AN:
151974
Hom.:
Cov.:
32
AF XY:
AC XY:
47076
AN XY:
74276
show subpopulations
African (AFR)
AF:
AC:
26052
AN:
41426
American (AMR)
AF:
AC:
9310
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
1938
AN:
3466
East Asian (EAS)
AF:
AC:
3338
AN:
5158
South Asian (SAS)
AF:
AC:
2622
AN:
4820
European-Finnish (FIN)
AF:
AC:
6940
AN:
10558
Middle Eastern (MID)
AF:
AC:
148
AN:
292
European-Non Finnish (NFE)
AF:
AC:
44361
AN:
67962
Other (OTH)
AF:
AC:
1275
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1808
3616
5425
7233
9041
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2240
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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