5-170106116-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012188.5(FOXI1):c.159C>T(p.Gly53Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,612,188 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 Uncertain significance (★).
Frequency
Consequence
NM_012188.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXI1 | NM_012188.5 | c.159C>T | p.Gly53Gly | synonymous_variant | Exon 1 of 2 | ENST00000306268.8 | NP_036320.2 | |
FOXI1 | NM_144769.4 | c.159C>T | p.Gly53Gly | synonymous_variant | Exon 1 of 2 | NP_658982.1 | ||
FOXI1 | XR_941092.2 | n.220C>T | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXI1 | ENST00000306268.8 | c.159C>T | p.Gly53Gly | synonymous_variant | Exon 1 of 2 | 1 | NM_012188.5 | ENSP00000304286.5 | ||
FOXI1 | ENST00000449804.4 | c.159C>T | p.Gly53Gly | synonymous_variant | Exon 1 of 2 | 1 | ENSP00000415483.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000821 AC: 2AN: 243460Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132668
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460054Hom.: 0 Cov.: 32 AF XY: 0.00000551 AC XY: 4AN XY: 726222
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74316
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with FOXI1-related conditions. 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 sequence change affects codon 53 of the FOXI1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the FOXI1 protein. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at