rs533176227

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_005263.5(GFI1):ā€‹c.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

Genomes: š‘“ 0.000085 ( 0 hom., cov: 34)
Exomes š‘“: 0.000092 ( 1 hom. )

Consequence

GFI1
NM_005263.5 missense

Scores

1
2
16

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:3

Conservation

PhyloP100: 3.50
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.048254132).
BS2
High AC in GnomAd4 at 13 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GFI1NM_005263.5 linkuse as main transcriptc.431C>G p.Ala144Gly missense_variant 4/7 ENST00000294702.6 NP_005254.2 Q99684

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GFI1ENST00000294702.6 linkuse as main transcriptc.431C>G p.Ala144Gly missense_variant 4/72 NM_005263.5 ENSP00000294702.5 Q99684
GFI1ENST00000370332.5 linkuse as main transcriptc.431C>G p.Ala144Gly missense_variant 4/71 ENSP00000359357.1 Q99684
GFI1ENST00000427103.6 linkuse as main transcriptc.431C>G p.Ala144Gly missense_variant 4/71 ENSP00000399719.1 Q99684

Frequencies

GnomAD3 genomes
AF:
0.0000854
AC:
13
AN:
152156
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000134
AC:
27
AN:
201000
Hom.:
0
AF XY:
0.000181
AC XY:
20
AN XY:
110302
show subpopulations
Gnomad AFR exome
AF:
0.0000887
Gnomad AMR exome
AF:
0.0000329
Gnomad ASJ exome
AF:
0.00123
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000370
Gnomad FIN exome
AF:
0.0000552
Gnomad NFE exome
AF:
0.0000235
Gnomad OTH exome
AF:
0.000196
GnomAD4 exome
AF:
0.0000924
AC:
133
AN:
1439078
Hom.:
1
Cov.:
34
AF XY:
0.000113
AC XY:
81
AN XY:
714056
show subpopulations
Gnomad4 AFR exome
AF:
0.0000303
Gnomad4 AMR exome
AF:
0.0000242
Gnomad4 ASJ exome
AF:
0.00101
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000348
Gnomad4 FIN exome
AF:
0.0000198
Gnomad4 NFE exome
AF:
0.0000599
Gnomad4 OTH exome
AF:
0.000151
GnomAD4 genome
AF:
0.0000854
AC:
13
AN:
152272
Hom.:
0
Cov.:
34
AF XY:
0.0000806
AC XY:
6
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000203
Hom.:
0
Bravo
AF:
0.000117
ExAC
AF:
0.000150
AC:
18

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 09, 2021The 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 submitterclinical testingGenetic Services Laboratory, University of ChicagoAug 30, 2016- -
Neutropenia, severe congenital, 2, autosomal dominant Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 24, 2023This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.51
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.16
T;T;T
Eigen
Benign
-0.42
Eigen_PC
Benign
-0.35
FATHMM_MKL
Benign
0.69
D
LIST_S2
Benign
0.79
.;T;.
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.048
T;T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
1.7
L;L;L
PrimateAI
Pathogenic
0.84
D
PROVEAN
Benign
-1.0
N;N;N
REVEL
Benign
0.055
Sift
Uncertain
0.0090
D;D;D
Sift4G
Benign
0.44
T;T;T
Polyphen
0.099
B;B;B
Vest4
0.13
MVP
0.69
MPC
0.65
ClinPred
0.055
T
GERP RS
3.1
Varity_R
0.19
gMVP
0.20

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs533176227; hg19: chr1-92946513; API