chr1-92478757-C-CAG
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_005263.5(GFI1):c.925-6_925-5dupCT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005263.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFI1 | ENST00000294702.6 | c.925-5_925-4insCT | splice_region_variant, intron_variant | Intron 5 of 6 | 2 | NM_005263.5 | ENSP00000294702.5 | |||
GFI1 | ENST00000370332.5 | c.925-5_925-4insCT | splice_region_variant, intron_variant | Intron 5 of 6 | 1 | ENSP00000359357.1 | ||||
GFI1 | ENST00000427103.6 | c.925-5_925-4insCT | splice_region_variant, intron_variant | Intron 5 of 6 | 1 | ENSP00000399719.1 | ||||
GFI1 | ENST00000696667.1 | c.138+1590_138+1591insCT | intron_variant | Intron 1 of 1 | ENSP00000512792.1 |
Frequencies
GnomAD3 genomes AF: 0.0978 AC: 13491AN: 137960Hom.: 948 Cov.: 0
GnomAD4 exome AF: 0.0659 AC: 88579AN: 1344604Hom.: 53 Cov.: 0 AF XY: 0.0661 AC XY: 44126AN XY: 667500
GnomAD4 genome AF: 0.0978 AC: 13498AN: 138066Hom.: 949 Cov.: 0 AF XY: 0.0973 AC XY: 6451AN XY: 66332
ClinVar
Submissions by phenotype
not specified Benign:2
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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not provided Benign:2
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GFI1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Neutropenia, severe congenital, 2, autosomal dominant Benign:1
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Nonimmune chronic idiopathic neutropenia of adults;C2751288:Neutropenia, severe congenital, 2, autosomal dominant Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at