Variant 9-92474742-CTCA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_017680.6(ASPN):c.153_155delTGA(p.Asp51del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.439 in 1,532,104 control chromosomes in the GnomAD database, including 124,043 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.40 ( 13265 hom., cov: 0)

Exomes 𝑓: 0.44 ( 110778 hom. )

Consequence

ASPN
NM_017680.6 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.52

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-92474742-CTCA-C is Benign according to our data. Variant chr9-92474742-CTCA-C is described in ClinVar as [Benign]. Clinvar id is 1302755.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-92474742-CTCA-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CENPP	NM_001012267.3 linkuse as main transcript	c.564+94925_564+94927delATC		intron_variant		ENST00000375587.8	NP_001012267.1	Q6IPU0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASPN	ENST00000375544.7 linkuse as main transcript	c.153_155delTGA	p.Asp51del	disruptive_inframe_deletion	2/8	1		ENSP00000364694.3		Q9BXN1
CENPP	ENST00000375587.8 linkuse as main transcript	c.564+94925_564+94927delATC		intron_variant		1	NM_001012267.3	ENSP00000364737.3		Q6IPU0-1

Frequencies

GnomAD3 genomes

AF:

0.400

AC:

58957

AN:

147384

Hom.:

13258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.434

Gnomad EAS

AF:

0.640

Gnomad SAS

AF:

0.449

Gnomad FIN

AF:

0.517

Gnomad MID

AF:

0.281

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.410

GnomAD4 exome

AF:

0.444

AC:

614369

AN:

1384612

Hom.:

110778

AF XY:

0.443

AC XY:

305192

AN XY:

689324

show subpopulations

Gnomad4 AFR exome

AF:

0.164

Gnomad4 AMR exome

AF:

0.493

Gnomad4 ASJ exome

AF:

0.403

Gnomad4 EAS exome

AF:

0.560

Gnomad4 SAS exome

AF:

0.413

Gnomad4 FIN exome

AF:

0.493

Gnomad4 NFE exome

AF:

0.448

Gnomad4 OTH exome

AF:

0.433

GnomAD4 genome

AF:

0.400

AC:

58985

AN:

147492

Hom.:

13265

Cov.:

AF XY:

0.405

AC XY:

29010

AN XY:

71690

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.434

Gnomad4 EAS

AF:

0.640

Gnomad4 SAS

AF:

0.448

Gnomad4 FIN

AF:

0.517

Gnomad4 NFE

AF:

0.476

Gnomad4 OTH

AF:

0.412

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 11, 2021

This variant is associated with the following publications: (PMID: 21329514) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over