6-1610477-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001453.3(FOXC1):c.32A>G(p.Asn11Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,475,002 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001453.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXC1 | NM_001453.3 | c.32A>G | p.Asn11Ser | missense_variant | Exon 1 of 1 | ENST00000645831.2 | NP_001444.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000133 AC: 2AN: 150566Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 1AN: 83494Hom.: 0 AF XY: 0.0000223 AC XY: 1AN XY: 44778
GnomAD4 exome AF: 0.0000136 AC: 18AN: 1324326Hom.: 0 Cov.: 31 AF XY: 0.0000108 AC XY: 7AN XY: 648580
GnomAD4 genome AF: 0.0000133 AC: 2AN: 150676Hom.: 0 Cov.: 31 AF XY: 0.0000272 AC XY: 2AN XY: 73596
ClinVar
Submissions by phenotype
Axenfeld-Rieger syndrome type 3 Uncertain:1
This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 11 of the FOXC1 protein (p.Asn11Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with FOXC1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1398433). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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