rs79452610
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005251.3(FOXC2):c.435C>T(p.Tyr145=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00153 in 1,614,160 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0078 ( 10 hom., cov: 33)
Exomes 𝑓: 0.00088 ( 20 hom. )
Consequence
FOXC2
NM_005251.3 synonymous
NM_005251.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.78
Genes affected
FOXC2 (HGNC:3801): (forkhead box C2) 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 may play a role in the development of mesenchymal tissues. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 16-86567770-C-T is Benign according to our data. Variant chr16-86567770-C-T is described in ClinVar as [Benign]. Clinvar id is 259696.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-86567770-C-T is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0078 (1188/152332) while in subpopulation AFR AF= 0.0267 (1109/41590). AF 95% confidence interval is 0.0254. There are 10 homozygotes in gnomad4. There are 567 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1188 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOXC2 | NM_005251.3 | c.435C>T | p.Tyr145= | synonymous_variant | 1/1 | ENST00000649859.1 | |
FOXC2-AS1 | NR_125795.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOXC2 | ENST00000649859.1 | c.435C>T | p.Tyr145= | synonymous_variant | 1/1 | NM_005251.3 | P1 | ||
FOXC2-AS1 | ENST00000563280.3 | n.78G>A | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00778 AC: 1184AN: 152214Hom.: 10 Cov.: 33
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GnomAD3 exomes AF: 0.00208 AC: 522AN: 251342Hom.: 4 AF XY: 0.00147 AC XY: 200AN XY: 135892
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GnomAD4 exome AF: 0.000882 AC: 1289AN: 1461828Hom.: 20 Cov.: 32 AF XY: 0.000778 AC XY: 566AN XY: 727212
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GnomAD4 genome ? AF: 0.00780 AC: 1188AN: 152332Hom.: 10 Cov.: 33 AF XY: 0.00761 AC XY: 567AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Feb 14, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at