6-1610015-GCC-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001453.3(FOXC1):c.-418_-417del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.027 ( 15 hom., cov: 13)
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
Not classified
Clinical Significance
Conservation
PhyloP100: 1.35
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 -2 ACMG points.
BP6
Variant 6-1610015-GCC-G is Benign according to our data. Variant chr6-1610015-GCC-G is described in ClinVar as [Benign]. Clinvar id is 1229415.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXC1 | NM_001453.3 | c.-418_-417del | 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.-418_-417del | 5_prime_UTR_variant | 1/1 | NM_001453.3 | ENSP00000493906 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2476AN: 92444Hom.: 15 Cov.: 13 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 128Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 94
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0268 AC: 2474AN: 92438Hom.: 15 Cov.: 13 AF XY: 0.0268 AC XY: 1161AN XY: 43350
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at