chr6-1610202-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001453.3(FOXC1):c.-244C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.013 in 152,226 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001453.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXC1 | ENST00000645831 | c.-244C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 1 | NM_001453.3 | ENSP00000493906.1 | ||||
FOXC1 | ENST00000645831 | c.-244C>T | 5_prime_UTR_variant | Exon 1 of 1 | NM_001453.3 | ENSP00000493906.1 |
Frequencies
GnomAD3 genomes AF: 0.0130 AC: 1978AN: 151612Hom.: 33 Cov.: 31
GnomAD4 exome AF: 0.00593 AC: 3AN: 506Hom.: 0 Cov.: 0 AF XY: 0.00806 AC XY: 2AN XY: 248
GnomAD4 genome AF: 0.0130 AC: 1976AN: 151720Hom.: 33 Cov.: 31 AF XY: 0.0132 AC XY: 981AN XY: 74168
ClinVar
Submissions by phenotype
not provided Pathogenic:1Benign:1
- -
See Variant Classification Assertion Criteria. -
Anterior segment dysgenesis 3 Benign:1
NG_009368.1(NM_001453.2):c.-244C>T in FOXC1 gene has an allele frequency of 0.041 in European (non-Finnish) subpopulation in the gnomAD database, including 27 homozygous occurrences. Taken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BS2. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at