chr9-92474742-C-CTCATCATCATCATCATCATCATCATCA
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_017680.6(ASPN):c.129_155dupTGATGATGATGATGATGATGATGATGA(p.Asp43_Asp51dup) variant causes a disruptive inframe insertion change. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
ASPN
NM_017680.6 disruptive_inframe_insertion
NM_017680.6 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.52
Publications
9 publications found
Genes affected
ASPN (HGNC:14872): (asporin) This gene encodes a cartilage extracellular protein that is member of the small leucine-rich proteoglycan family. The encoded protein may regulate chondrogenesis by inhibiting transforming growth factor-beta 1-induced gene expression in cartilage. This protein also binds collagen and calcium and may induce collagen mineralization. Polymorphisms in the aspartic acid repeat region of this gene are associated with a susceptibility to osteoarthritis, and also with intervertebral disc disease. Alternative splicing of this gene results in multiple transcript variants.[provided by RefSeq, Jul 2014]
CENPP (HGNC:32933): (centromere protein P) CENPP is a subunit of a CENPH (MIM 605607)-CENPI (MIM 300065)-associated centromeric complex that targets CENPA (MIM 117139) to centromeres and is required for proper kinetochore function and mitotic progression (Okada et al., 2006 [PubMed 16622420]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_017680.6
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_017680.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ASPN | MANE Select | c.129_155dupTGATGATGATGATGATGATGATGATGA | p.Asp43_Asp51dup | disruptive_inframe_insertion | Exon 2 of 8 | NP_060150.4 | |||
| CENPP | MANE Select | c.564+94901_564+94927dupATCATCATCATCATCATCATCATCATC | intron | N/A | NP_001012267.1 | Q6IPU0-1 | |||
| ASPN | c.129_155dupTGATGATGATGATGATGATGATGATGA | p.Asp43_Asp51dup | disruptive_inframe_insertion | Exon 2 of 6 | NP_001180264.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ASPN | TSL:1 | c.129_155dupTGATGATGATGATGATGATGATGATGA | p.Asp43_Asp51dup | disruptive_inframe_insertion | Exon 2 of 8 | ENSP00000364694.3 | Q9BXN1 | ||
| CENPP | TSL:1 MANE Select | c.564+94901_564+94927dupATCATCATCATCATCATCATCATCATC | intron | N/A | ENSP00000364737.3 | Q6IPU0-1 | |||
| ASPN | c.129_155dupTGATGATGATGATGATGATGATGATGA | p.Asp43_Asp51dup | disruptive_inframe_insertion | Exon 3 of 9 | ENSP00000577527.1 |
Frequencies
GnomAD3 genomes 0.00000678 AC: 1AN: 147588Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
147588
Hom.:
Cov.:
0
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: 0.00000144 AC: 2AN: 1387046Hom.: 0 Cov.: 0 AF XY: 0.00000145 AC XY: 1AN XY: 690652 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1387046
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
690652
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30720
American (AMR)
AF:
AC:
0
AN:
41068
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24902
East Asian (EAS)
AF:
AC:
0
AN:
37702
South Asian (SAS)
AF:
AC:
0
AN:
81708
European-Finnish (FIN)
AF:
AC:
0
AN:
50526
Middle Eastern (MID)
AF:
AC:
0
AN:
5576
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1057302
Other (OTH)
AF:
AC:
0
AN:
57542
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000678 AC: 1AN: 147588Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 71680 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
147588
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
71680
show subpopulations
African (AFR)
AF:
AC:
0
AN:
39564
American (AMR)
AF:
AC:
0
AN:
14670
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3432
East Asian (EAS)
AF:
AC:
0
AN:
5002
South Asian (SAS)
AF:
AC:
0
AN:
4568
European-Finnish (FIN)
AF:
AC:
0
AN:
9962
Middle Eastern (MID)
AF:
AC:
0
AN:
310
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67178
Other (OTH)
AF:
AC:
0
AN:
2004
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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