rs387906276

Positions:

• chr9-92474742-C-CTCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCA-C
• chr9-92474742-CTCATCATCATCATCATCATCATCA-C
• chr9-92474742-C-CTCATCATCATCA
• chr9-92474742-CTCATCATCATCATCA-C
• chr9-92474742-C-CTCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCA-C
• chr9-92474742-C-CTCATCATCATCATCATCATCA
• chr9-92474742-C-CTCA
• chr9-92474742-C-CTCATCA
• chr9-92474742-C-CTCATCATCA
• chr9-92474742-CTCATCATCA-C
• chr9-92474742-CTCATCATCATCATCATCA-C
• chr9-92474742-C-CTCATCATCATCATCATCA
• chr9-92474742-CTCATCA-C
• chr9-92474742-CTCATCATCATCA-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The ENST00000375544.7(ASPN):​c.155_156insTGATGATGATGATGA​(p.Asp47_Asp51dup) variant causes a inframe insertion change. 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 ENST00000375544.7 inframe_insertion
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.52

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 9-92474742-C-CTCATCATCATCATCA is Benign according to our data. Variant chr9-92474742-C-CTCATCATCATCATCA is described in ClinVar 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/exons	MANE	UniProt
ASPN	NM_017680.6	c.155_156insTGATGATGATGATGA	p.Asp47_Asp51dup	inframe_insertion	2/8	ENST00000710274.1
ASPN	NM_001193335.3	c.155_156insTGATGATGATGATGA	p.Asp47_Asp51dup	inframe_insertion	2/6
CENPP	NM_001012267.3	c.564+94913_564+94927dup		intron_variant		ENST00000375587.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASPN	ENST00000375544.7	c.155_156insTGATGATGATGATGA	p.Asp47_Asp51dup	inframe_insertion	2/8	1		P1
CENPP	ENST00000375587.8	c.564+94913_564+94927dup		intron_variant		1	NM_001012267.3	P1

Frequencies

GnomAD3 genomes AF: 0.000102 AC: 15 AN: 147588 Hom.: 0 Cov.: 0

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.: 0 Cov.: 0 AF XY: 0.000188 AC XY: 130 AN XY: 690642

Gnomad4 AFR exome AF: 0.000130

Gnomad4 AMR exome AF: 0.0000974

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000637

Gnomad4 SAS exome AF: 0.000196

Gnomad4 FIN exome AF: 0.000139

Gnomad4 NFE exome AF: 0.000171

Gnomad4 OTH exome AF: 0.000122

GnomAD4 genome AF: 0.000102 AC: 15 AN: 147694 Hom.: 0 Cov.: 0 AF XY: 0.0000975 AC XY: 7 AN XY: 71800

Gnomad4 AFR AF: 0.000101

Gnomad4 AMR AF: 0.0000681

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000200

Gnomad4 SAS AF: 0.000657

Gnomad4 FIN AF: 0.000100

Gnomad4 NFE AF: 0.0000744

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 05, 2021

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

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3078372; hg19: chr9-95237024;