7-144397690-A-G
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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.1775-149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 668,566 control chromosomes in the GnomAD database, including 117,744 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.59 ( 27372 hom., cov: 32)
Exomes 𝑓: 0.58 ( 90372 hom. )
Consequence
NOBOX
NM_001080413.3 intron
NM_001080413.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.269
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=-0.9).
BP6
Variant 7-144397690-A-G is Benign according to our data. Variant chr7-144397690-A-G is described in ClinVar as [Benign]. Clinvar id is 1248530.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOBOX | NM_001080413.3 | c.1775-149T>C | intron_variant | ENST00000467773.1 | NP_001073882.3 | |||
NOBOX | XM_017011742.3 | c.1679-149T>C | intron_variant | XP_016867231.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOBOX | ENST00000467773.1 | c.1775-149T>C | intron_variant | 5 | NM_001080413.3 | ENSP00000419457.1 | ||||
NOBOX | ENST00000483238.5 | c.1679-149T>C | intron_variant | 5 | ENSP00000419565.1 | |||||
NOBOX | ENST00000645489.1 | c.1424-149T>C | intron_variant | ENSP00000496732.1 | ||||||
NOBOX | ENST00000643164.1 | c.872-149T>C | intron_variant | ENSP00000495343.1 |
Frequencies
GnomAD3 genomes AF: 0.594 AC: 90292AN: 151890Hom.: 27335 Cov.: 32
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GnomAD4 exome AF: 0.580 AC: 299804AN: 516558Hom.: 90372 AF XY: 0.592 AC XY: 157847AN XY: 266784
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GnomAD4 genome AF: 0.595 AC: 90384AN: 152008Hom.: 27372 Cov.: 32 AF XY: 0.600 AC XY: 44564AN XY: 74316
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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 | clinical testing | GeneDx | Jun 26, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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