1-92478757-CAGAGAGAGAGAGAGAGAGAGAG-CAGAG
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_005263.5(GFI1):c.925-22_925-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,520,824 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
GFI1
NM_005263.5 splice_region, splice_polypyrimidine_tract, intron
NM_005263.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.17
Genes affected
GFI1 (HGNC:4237): (growth factor independent 1 transcriptional repressor) This gene encodes a nuclear zinc finger protein that functions as a transcriptional repressor. This protein plays a role in diverse developmental contexts, including hematopoiesis and oncogenesis. It functions as part of a complex along with other cofactors to control histone modifications that lead to silencing of the target gene promoters. Mutations in this gene cause autosomal dominant severe congenital neutropenia, and also dominant nonimmune chronic idiopathic neutropenia of adults, which are heterogeneous hematopoietic disorders that cause predispositions to leukemias and infections. Multiple alternatively spliced variants, encoding the same protein, have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFI1 | NM_005263.5 | c.925-22_925-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000294702.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFI1 | ENST00000294702.6 | c.925-22_925-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_005263.5 | P1 | |||
GFI1 | ENST00000370332.5 | c.925-22_925-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
GFI1 | ENST00000427103.6 | c.925-22_925-5del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
GFI1 | ENST00000696667.1 | c.138+1573_138+1590del | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000145 AC: 2AN: 138180Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000101 AC: 14AN: 1382644Hom.: 0 AF XY: 0.0000131 AC XY: 9AN XY: 686992
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GnomAD4 genome ? AF: 0.0000145 AC: 2AN: 138180Hom.: 0 Cov.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66324
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at