rs7800847
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001080413.3(NOBOX):c.349C>T(p.Arg117Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00423 in 1,515,074 control chromosomes in the GnomAD database, including 236 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001080413.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOBOX | NM_001080413.3 | c.349C>T | p.Arg117Trp | missense_variant | 4/10 | ENST00000467773.1 | |
NOBOX | XM_017011742.3 | c.349C>T | p.Arg117Trp | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOBOX | ENST00000467773.1 | c.349C>T | p.Arg117Trp | missense_variant | 4/10 | 5 | NM_001080413.3 | ||
NOBOX | ENST00000483238.5 | c.349C>T | p.Arg117Trp | missense_variant | 4/10 | 5 | A2 | ||
NOBOX | ENST00000645489.1 | c.94C>T | p.Arg32Trp | missense_variant | 2/8 | P2 | |||
NOBOX | ENST00000643164.1 | c.38-1229C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0221 AC: 3362AN: 152182Hom.: 122 Cov.: 33
GnomAD3 exomes AF: 0.00687 AC: 1144AN: 166522Hom.: 37 AF XY: 0.00514 AC XY: 458AN XY: 89040
GnomAD4 exome AF: 0.00224 AC: 3051AN: 1362774Hom.: 114 Cov.: 31 AF XY: 0.00199 AC XY: 1332AN XY: 667756
GnomAD4 genome ? AF: 0.0221 AC: 3364AN: 152300Hom.: 122 Cov.: 33 AF XY: 0.0215 AC XY: 1600AN XY: 74478
ClinVar
Submissions by phenotype
Premature ovarian failure 5 Pathogenic:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 10, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2011 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 24, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 05, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Premature ovarian failure 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at