9-92474742-C-CTCATCATCATCATCA

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001193335.3(ASPN):c.141_155dupTGATGATGATGATGA(p.Asp47_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. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00010 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00018 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ASPN
NM_001193335.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.52

Publications

9 publications found

Variant links:

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]

ASPN links:

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]

CENPP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

BP6

Variant 9-92474742-C-CTCATCATCATCATCA is Benign according to our data. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-C-CTCATCATCATCATCA is described in CliVar as Benign. Clinvar id is 1248251.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENPP	NM_001012267.3 link	c.564+94913_564+94927dupATCATCATCATCATC		intron_variant	Intron 5 of 7	ENST00000375587.8	NP_001012267.1	Q6IPU0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASPN	ENST00000375544.7 link	c.141_155dupTGATGATGATGATGA	p.Asp47_Asp51dup	disruptive_inframe_insertion	Exon 2 of 8	1		ENSP00000364694.3		Q9BXN1
CENPP	ENST00000375587.8 link	c.564+94913_564+94927dupATCATCATCATCATC		intron_variant	Intron 5 of 7	1	NM_001012267.3	ENSP00000364737.3		Q6IPU0-1

Frequencies

GnomAD3 genomes

AF:

0.000102

AC:

AN:

147588

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000682

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000200

Gnomad SAS

AF:

0.000657

Gnomad FIN

AF:

0.000100

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000744

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000175

AC:

243

AN:

1387020

Hom.:

Cov.:

AF XY:

0.000188

AC XY:

130

AN XY:

690642

show subpopulations

African (AFR)

AF:

0.000130

AC:

AN:

30720

American (AMR)

AF:

0.0000974

AC:

AN:

41068

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24902

East Asian (EAS)

AF:

0.000637

AC:

AN:

37702

South Asian (SAS)

AF:

0.000196

AC:

AN:

81706

European-Finnish (FIN)

AF:

0.000139

AC:

AN:

50526

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5576

European-Non Finnish (NFE)

AF:

0.000171

AC:

181

AN:

1057278

Other (OTH)

AF:

0.000122

AC:

AN:

57542

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.436

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000102

AC:

AN:

147694

Hom.:

Cov.:

AF XY:

0.0000975

AC XY:

AN XY:

71800

show subpopulations

African (AFR)

AF:

0.000101

AC:

AN:

39674

American (AMR)

AF:

0.0000681

AC:

AN:

14690

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3432

East Asian (EAS)

AF:

0.000200

AC:

AN:

4990

South Asian (SAS)

AF:

0.000657

AC:

AN:

4564

European-Finnish (FIN)

AF:

0.000100

AC:

AN:

9962

Middle Eastern (MID)

AF:

0.00

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.0000744

AC:

AN:

67170

Other (OTH)

AF:

0.00

AC:

AN:

2026

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.548

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

224

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Mar 05, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

4.5

Mutation Taster

=79/21

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over