1-92476053-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_005263.5(GFI1):c.1245G>T(p.Arg415Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R415R) has been classified as Likely benign.
Frequency
Consequence
NM_005263.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFI1 | ENST00000294702.6 | c.1245G>T | p.Arg415Arg | synonymous_variant | 7/7 | 2 | NM_005263.5 | ENSP00000294702.5 | ||
GFI1 | ENST00000370332.5 | c.1245G>T | p.Arg415Arg | synonymous_variant | 7/7 | 1 | ENSP00000359357.1 | |||
GFI1 | ENST00000427103.6 | c.1245G>T | p.Arg415Arg | synonymous_variant | 7/7 | 1 | ENSP00000399719.1 | |||
GFI1 | ENST00000696667.1 | c.293G>T | p.Gly98Val | missense_variant | 2/2 | ENSP00000512792.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251044Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135732
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461802Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727196
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Neutropenia, severe congenital, 2, autosomal dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at