chr17-76140135-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001454.4(FOXJ1):c.261G>A(p.Thr87Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000876 in 1,575,312 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000090 ( 3 hom. )
Consequence
FOXJ1
NM_001454.4 synonymous
NM_001454.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.17
Genes affected
FOXJ1 (HGNC:3816): (forkhead box J1) This gene encodes a member of the forkhead family of transcription factors. Similar genes in zebrafish and mouse have been shown to regulate the transcription of genes that control the production of motile cilia. The mouse ortholog also functions in the determination of left-right asymmetry. Polymorphisms in this gene are associated with systemic lupus erythematosus and allergic rhinitis.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 17-76140135-C-T is Benign according to our data. Variant chr17-76140135-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3777921.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXJ1 | NM_001454.4 | c.261G>A | p.Thr87Thr | synonymous_variant | Exon 2 of 3 | ENST00000322957.7 | NP_001445.2 | |
FOXJ1 | XM_047435666.1 | c.261G>A | p.Thr87Thr | synonymous_variant | Exon 1 of 2 | XP_047291622.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000659 AC: 10AN: 151784Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000203 AC: 37AN: 182494Hom.: 2 AF XY: 0.000276 AC XY: 28AN XY: 101576
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GnomAD4 exome AF: 0.0000899 AC: 128AN: 1423412Hom.: 3 Cov.: 33 AF XY: 0.000136 AC XY: 96AN XY: 706758
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GnomAD4 genome AF: 0.0000658 AC: 10AN: 151900Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74266
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
FOXJ1: BP4, BP7 -
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at