rs757388
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001080413.3(NOBOX):c.1154+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 1,591,958 control chromosomes in the GnomAD database, including 287,660 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.61 ( 28921 hom., cov: 33)
Exomes 𝑓: 0.60 ( 258739 hom. )
Consequence
NOBOX
NM_001080413.3 intron
NM_001080413.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.185
Genes affected
NOBOX (HGNC:22448): (NOBOX oogenesis homeobox) This homeobox gene encodes a transcription factor that is thought to play a role in oogenesis. In mice, it is essential for folliculogenesis and regulation of oocyte-specific genes. Defects in this gene result in premature ovarian failure type 5.[provided by RefSeq, May 2011]
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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=-0.85).
BP6
?
Variant 7-144399746-A-G is Benign according to our data. Variant chr7-144399746-A-G is described in ClinVar as [Benign]. Clinvar id is 359144.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-144399746-A-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOBOX | NM_001080413.3 | c.1154+11T>C | intron_variant | ENST00000467773.1 | |||
NOBOX | XM_017011742.3 | c.1058+11T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NOBOX | ENST00000467773.1 | c.1154+11T>C | intron_variant | 5 | NM_001080413.3 | ||||
NOBOX | ENST00000483238.5 | c.1058+11T>C | intron_variant | 5 | A2 | ||||
NOBOX | ENST00000643164.1 | c.251+11T>C | intron_variant | ||||||
NOBOX | ENST00000645489.1 | c.803+11T>C | intron_variant | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.612 AC: 93023AN: 151994Hom.: 28891 Cov.: 33
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GnomAD3 exomes AF: 0.633 AC: 145869AN: 230290Hom.: 47262 AF XY: 0.640 AC XY: 79460AN XY: 124222
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GnomAD4 exome AF: 0.595 AC: 856852AN: 1439846Hom.: 258739 Cov.: 30 AF XY: 0.602 AC XY: 430378AN XY: 714978
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GnomAD4 genome ? AF: 0.612 AC: 93105AN: 152112Hom.: 28921 Cov.: 33 AF XY: 0.617 AC XY: 45886AN XY: 74358
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Premature ovarian failure 5 Benign:2
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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at