rs1284257748
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3
The NM_007363.5(NONO):c.84_95delCCACCAGCAGCA(p.His28_Gln31del) variant causes a disruptive inframe deletion 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 DEL_BIG, 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)
Exomes 𝑓: 0.0000037 ( 0 hom. 1 hem. )
Failed GnomAD Quality Control
Consequence
NONO
NM_007363.5 disruptive_inframe_deletion
NM_007363.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.33
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 disorderInheritance: XL Classification: DEFINITIVE Submitted by: Ambry Genetics
- X-linked syndromic intellectual disabilityInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- syndromic X-linked intellectual disability 34Inheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_007363.5
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 | MANE Select | c.84_95delCCACCAGCAGCA | p.His28_Gln31del | disruptive_inframe_deletion | Exon 3 of 12 | NP_031389.3 | |||
| NONO | c.84_95delCCACCAGCAGCA | p.His28_Gln31del | disruptive_inframe_deletion | Exon 4 of 13 | NP_001138880.1 | A0A0S2Z4Z9 | |||
| NONO | c.84_95delCCACCAGCAGCA | p.His28_Gln31del | disruptive_inframe_deletion | Exon 2 of 11 | NP_001138881.1 | Q15233-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NONO | TSL:1 MANE Select | c.84_95delCCACCAGCAGCA | p.His28_Gln31del | disruptive_inframe_deletion | Exon 3 of 12 | ENSP00000276079.8 | Q15233-1 | ||
| NONO | TSL:1 | c.84_95delCCACCAGCAGCA | p.His28_Gln31del | disruptive_inframe_deletion | Exon 3 of 13 | ENSP00000362963.4 | A0A7P0MRW0 | ||
| NONO | TSL:1 | c.84_95delCCACCAGCAGCA | p.His28_Gln31del | disruptive_inframe_deletion | Exon 2 of 11 | ENSP00000362947.1 | Q15233-1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000367 AC: 4AN: 1089297Hom.: 0 AF XY: 0.00000281 AC XY: 1AN XY: 355537 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
4
AN:
1089297
Hom.:
AF XY:
AC XY:
1
AN XY:
355537
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
26184
American (AMR)
AF:
AC:
0
AN:
34559
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19163
East Asian (EAS)
AF:
AC:
0
AN:
30010
South Asian (SAS)
AF:
AC:
1
AN:
53103
European-Finnish (FIN)
AF:
AC:
0
AN:
40108
Middle Eastern (MID)
AF:
AC:
0
AN:
4100
European-Non Finnish (NFE)
AF:
AC:
2
AN:
836350
Other (OTH)
AF:
AC:
1
AN:
45720
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000343967), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.392
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
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0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
23
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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