5-170105965-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012188.5(FOXI1):c.8C>T(p.Ser3Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000621 in 1,609,724 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 (★). Synonymous variant affecting the same amino acid position (i.e. S3S) has been classified as Likely benign.
Frequency
Consequence
NM_012188.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXI1 | NM_012188.5 | c.8C>T | p.Ser3Phe | missense_variant | 1/2 | ENST00000306268.8 | |
FOXI1 | NM_144769.4 | c.8C>T | p.Ser3Phe | missense_variant | 1/2 | ||
FOXI1 | XR_941092.2 | n.69C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXI1 | ENST00000306268.8 | c.8C>T | p.Ser3Phe | missense_variant | 1/2 | 1 | NM_012188.5 | P1 | |
FOXI1 | ENST00000449804.4 | c.8C>T | p.Ser3Phe | missense_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241702Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132106
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1457596Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 2AN XY: 724798
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.8C>T (p.S3F) alteration is located in exon 1 (coding exon 1) of the FOXI1 gene. This alteration results from a C to T substitution at nucleotide position 8, causing the serine (S) at amino acid position 3 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at