rs150506480
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_005263.5(GFI1):c.115+10_115+29del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,285,568 control chromosomes in the GnomAD database, including 271 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.026 ( 130 hom., cov: 32)
Exomes 𝑓: 0.010 ( 141 hom. )
Consequence
GFI1
NM_005263.5 intron
NM_005263.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.82
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 Benign. Variant got -16 ACMG points.
BP6
?
Variant 1-92483343-AGCCCCGCCTGGCCCGCGCGC-A is Benign according to our data. Variant chr1-92483343-AGCCCCGCCTGGCCCGCGCGC-A is described in ClinVar as [Benign]. Clinvar id is 259700.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0717 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GFI1 | NM_005263.5 | c.115+10_115+29del | intron_variant | ENST00000294702.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFI1 | ENST00000294702.6 | c.115+10_115+29del | intron_variant | 2 | NM_005263.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0259 AC: 3934AN: 152110Hom.: 130 Cov.: 32
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GnomAD3 exomes AF: 0.0113 AC: 2575AN: 227540Hom.: 57 AF XY: 0.00965 AC XY: 1196AN XY: 123876
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GnomAD4 exome AF: 0.0101 AC: 11446AN: 1133340Hom.: 141 AF XY: 0.00956 AC XY: 5527AN XY: 577904
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GnomAD4 genome ? AF: 0.0259 AC: 3937AN: 152228Hom.: 130 Cov.: 32 AF XY: 0.0246 AC XY: 1831AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Neutropenia, severe congenital, 2, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at