chrX-71290941-G-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_007363.5(NONO):c.154+150G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00459 in 660,145 control chromosomes in the GnomAD database, including 68 homozygotes. There are 713 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 41 hom., 483 hem., cov: 24)
Exomes 𝑓: 0.0021 ( 27 hom. 230 hem. )
Consequence
NONO
NM_007363.5 intron
NM_007363.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.655
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant X-71290941-G-C is Benign according to our data. Variant chrX-71290941-G-C is described in ClinVar as [Benign]. Clinvar id is 1245268.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NONO | NM_007363.5 | c.154+150G>C | intron_variant | ENST00000276079.13 | NP_031389.3 | |||
NONO | NM_001145408.2 | c.154+150G>C | intron_variant | NP_001138880.1 | ||||
NONO | NM_001145409.2 | c.154+150G>C | intron_variant | NP_001138881.1 | ||||
NONO | NM_001145410.2 | c.-113-838G>C | intron_variant | NP_001138882.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NONO | ENST00000276079.13 | c.154+150G>C | intron_variant | 1 | NM_007363.5 | ENSP00000276079 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0168 AC: 1878AN: 112083Hom.: 41 Cov.: 24 AF XY: 0.0140 AC XY: 478AN XY: 34255
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GnomAD4 exome AF: 0.00209 AC: 1148AN: 548007Hom.: 27 AF XY: 0.00195 AC XY: 230AN XY: 118207
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GnomAD4 genome AF: 0.0168 AC: 1884AN: 112138Hom.: 41 Cov.: 24 AF XY: 0.0141 AC XY: 483AN XY: 34320
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at