X-71290724-CCAGCAGCAACAG-GCAGCAGCACCAC

Variant names:

• chrX-71290724-CCAGCAGCAACAG-GCAGCAGCACCAC
• NM_007363.5:c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC

Variant summary

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

The NM_007363.5(NONO):​c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC​(p.HisGlnGlnGlnGln29GlnGlnGlnHisHis) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: NONO NM_007363.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.52
• Publications: 0 publications found

Genes affected

NONO (HGNC:7871): (non-POU domain containing octamer binding) This gene encodes an RNA-binding protein which plays various roles in the nucleus, including transcriptional regulation and RNA splicing. A rearrangement between this gene and the transcription factor E3 gene has been observed in papillary renal cell carcinoma. Alternatively spliced transcript variants have been described. Pseudogenes exist on Chromosomes 2 and 16. [provided by RefSeq, Feb 2009]

NONO Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: XL Classification: DEFINITIVE Submitted by: Ambry Genetics
• X-linked syndromic intellectual disability

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• syndromic X-linked intellectual disability 34

  Inheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007363.5. 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
	NONO	NM_007363.5	MANE Select	c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC	p.HisGlnGlnGlnGln29GlnGlnGlnHisHis	missense	N/A	NP_031389.3
	NONO	NM_001145408.2		c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC	p.HisGlnGlnGlnGln29GlnGlnGlnHisHis	missense	N/A	NP_001138880.1	A0A0S2Z4Z9
	NONO	NM_001145409.2		c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC	p.HisGlnGlnGlnGln29GlnGlnGlnHisHis	missense	N/A	NP_001138881.1	Q15233-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NONO	ENST00000276079.13	TSL:1 MANE Select	c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC	p.HisGlnGlnGlnGln29GlnGlnGlnHisHis	missense	N/A	ENSP00000276079.8	Q15233-1
	NONO	ENST00000373856.8	TSL:1	c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC	p.HisGlnGlnGlnGln29GlnGlnGlnHisHis	missense	N/A	ENSP00000362963.4	A0A7P0MRW0
	NONO	ENST00000373841.5	TSL:1	c.87_99delCCAGCAGCAACAGinsGCAGCAGCACCAC	p.HisGlnGlnGlnGln29GlnGlnGlnHisHis	missense	N/A	ENSP00000362947.1	Q15233-1

Frequencies

GnomAD3 genomes Cov.: 23

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.5

Splicing

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

Other links and lift over

hg19: chrX-70510574;