chrX-71290941-G-C

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.655
Variant links:
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
NONONM_007363.5 linkuse as main transcriptc.154+150G>C intron_variant ENST00000276079.13 NP_031389.3
NONONM_001145408.2 linkuse as main transcriptc.154+150G>C intron_variant NP_001138880.1
NONONM_001145409.2 linkuse as main transcriptc.154+150G>C intron_variant NP_001138881.1
NONONM_001145410.2 linkuse as main transcriptc.-113-838G>C intron_variant NP_001138882.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NONOENST00000276079.13 linkuse as main transcriptc.154+150G>C intron_variant 1 NM_007363.5 ENSP00000276079 P1Q15233-1

Frequencies

GnomAD3 genomes
AF:
0.0168
AC:
1878
AN:
112083
Hom.:
41
Cov.:
24
AF XY:
0.0140
AC XY:
478
AN XY:
34255
show subpopulations
Gnomad AFR
AF:
0.0571
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00766
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000366
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00418
Gnomad NFE
AF:
0.000338
Gnomad OTH
AF:
0.0133
GnomAD4 exome
AF:
0.00209
AC:
1148
AN:
548007
Hom.:
27
AF XY:
0.00195
AC XY:
230
AN XY:
118207
show subpopulations
Gnomad4 AFR exome
AF:
0.0645
Gnomad4 AMR exome
AF:
0.00430
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000481
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000229
Gnomad4 OTH exome
AF:
0.00629
GnomAD4 genome
AF:
0.0168
AC:
1884
AN:
112138
Hom.:
41
Cov.:
24
AF XY:
0.0141
AC XY:
483
AN XY:
34320
show subpopulations
Gnomad4 AFR
AF:
0.0572
Gnomad4 AMR
AF:
0.00765
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000368
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000338
Gnomad4 OTH
AF:
0.0131
Alfa
AF:
0.0123
Hom.:
38
Bravo
AF:
0.0198

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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMay 13, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
2.8
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5980751; hg19: chrX-70510791; API