rs533176227
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005263.5(GFI1):āc.431C>Gā(p.Ala144Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000917 in 1,591,350 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_005263.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GFI1 | NM_005263.5 | c.431C>G | p.Ala144Gly | missense_variant | 4/7 | ENST00000294702.6 | NP_005254.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFI1 | ENST00000294702.6 | c.431C>G | p.Ala144Gly | missense_variant | 4/7 | 2 | NM_005263.5 | ENSP00000294702.5 | ||
GFI1 | ENST00000370332.5 | c.431C>G | p.Ala144Gly | missense_variant | 4/7 | 1 | ENSP00000359357.1 | |||
GFI1 | ENST00000427103.6 | c.431C>G | p.Ala144Gly | missense_variant | 4/7 | 1 | ENSP00000399719.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152156Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000134 AC: 27AN: 201000Hom.: 0 AF XY: 0.000181 AC XY: 20AN XY: 110302
GnomAD4 exome AF: 0.0000924 AC: 133AN: 1439078Hom.: 1 Cov.: 34 AF XY: 0.000113 AC XY: 81AN XY: 714056
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152272Hom.: 0 Cov.: 34 AF XY: 0.0000806 AC XY: 6AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.431C>G (p.A144G) alteration is located in exon 4 (coding exon 3) of the GFI1 gene. This alteration results from a C to G substitution at nucleotide position 431, causing the alanine (A) at amino acid position 144 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 30, 2016 | - - |
Neutropenia, severe congenital, 2, autosomal dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 24, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 144 of the GFI1 protein (p.Ala144Gly). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with GFI1-related conditions. ClinVar contains an entry for this variant (Variation ID: 435318). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GFI1 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at