rs3078372

Variant names:

• chr9-92474742-CTCATCATCATCATCATCATCATCA-C
• rs3078372
• ENST00000375544.7:c.132_155delTGATGATGATGATGATGATGATGA

Your query was ambiguous. Multiple possible variants found:

• chr9-92474742-CTCATCATCATCATCATCATCATCA-C
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA
• chr9-92474742-CTCATCATCATCATCATCATCATCA-CTCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCATCA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000375544.7(ASPN):​c.132_155delTGATGATGATGATGATGATGATGA​(p.Asp44_Asp51del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000873 in 1,534,632 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_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. Synonymous variant affecting the same amino acid position (i.e. D44D) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000047 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000092 (0 hom.)
• Consequence: ASPN ENST00000375544.7 disruptive_inframe_deletion
• 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENPP	NM_001012267.3	c.564+94904_564+94927delATCATCATCATCATCATCATCATC		intron_variant	Intron 5 of 7	ENST00000375587.8	NP_001012267.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASPN	ENST00000375544.7	c.132_155delTGATGATGATGATGATGATGATGA	p.Asp44_Asp51del	disruptive_inframe_deletion	Exon 2 of 8	1		ENSP00000364694.3
CENPP	ENST00000375587.8	c.564+94904_564+94927delATCATCATCATCATCATCATCATC		intron_variant	Intron 5 of 7	1	NM_001012267.3	ENSP00000364737.3

Frequencies

GnomAD3 genomes AF: 0.0000474 AC: 7 AN: 147588 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000253

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000893

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000916 AC: 127 AN: 1387044 Hom.: 0 AF XY: 0.0000999 AC XY: 69 AN XY: 690652

African (AFR) AF: 0.00 AC: 0 AN: 30720

American (AMR) AF: 0.0000243 AC: 1 AN: 41068

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24902

East Asian (EAS) AF: 0.00 AC: 0 AN: 37702

South Asian (SAS) AF: 0.00 AC: 0 AN: 81708

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50524

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5576

European-Non Finnish (NFE) AF: 0.000119 AC: 126 AN: 1057302

Other (OTH) AF: 0.00 AC: 0 AN: 57542

GnomAD4 genome AF: 0.0000474 AC: 7 AN: 147588 Hom.: 0 Cov.: 0 AF XY: 0.0000279 AC XY: 2 AN XY: 71680

African (AFR) AF: 0.0000253 AC: 1 AN: 39564

American (AMR) AF: 0.00 AC: 0 AN: 14670

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3432

East Asian (EAS) AF: 0.00 AC: 0 AN: 5002

South Asian (SAS) AF: 0.00 AC: 0 AN: 4568

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9962

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 310

European-Non Finnish (NFE) AF: 0.0000893 AC: 6 AN: 67178

Other (OTH) AF: 0.00 AC: 0 AN: 2004

Alfa AF: 0.00 Hom.: 224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.5
Mutation Taster		=157/43	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3078372; hg19: chr9-95237024;