6-1610013-C-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001453.3(FOXC1):c.-433C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00010 ( 0 hom., cov: 25)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FOXC1
NM_001453.3 5_prime_UTR
NM_001453.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.517
Genes affected
FOXC1 (HGNC:3800): (forkhead box C1) This gene belongs to the forkhead family of transcription factors which is characterized by a distinct DNA-binding forkhead domain. The specific function of this gene has not yet been determined; however, it has been shown to play a role in the regulation of embryonic and ocular development. Mutations in this gene cause various glaucoma phenotypes including primary congenital glaucoma, autosomal dominant iridogoniodysgenesis anomaly, and Axenfeld-Rieger anomaly. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 6-1610013-C-G is Benign according to our data. Variant chr6-1610013-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3031842.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXC1 | NM_001453.3 | c.-433C>G | 5_prime_UTR_variant | 1/1 | ENST00000645831.2 | NP_001444.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOXC1 | ENST00000645831.2 | c.-433C>G | 5_prime_UTR_variant | 1/1 | NM_001453.3 | ENSP00000493906 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 10AN: 98768Hom.: 0 Cov.: 25 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 224Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 180
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000101 AC: 10AN: 98828Hom.: 0 Cov.: 25 AF XY: 0.0000630 AC XY: 3AN XY: 47594
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
FOXC1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 31, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at