17-76140117-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_001454.4(FOXJ1):c.279G>A(p.Ser93Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000855 in 1,590,782 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001454.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOXJ1 | NM_001454.4 | c.279G>A | p.Ser93Ser | synonymous_variant | Exon 2 of 3 | ENST00000322957.7 | NP_001445.2 | |
FOXJ1 | XM_047435666.1 | c.279G>A | p.Ser93Ser | synonymous_variant | Exon 1 of 2 | XP_047291622.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000939 AC: 14AN: 149066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000842 AC: 18AN: 213702Hom.: 0 AF XY: 0.0000930 AC XY: 11AN XY: 118296
GnomAD4 exome AF: 0.0000846 AC: 122AN: 1441716Hom.: 1 Cov.: 33 AF XY: 0.0000837 AC XY: 60AN XY: 717174
GnomAD4 genome AF: 0.0000939 AC: 14AN: 149066Hom.: 0 Cov.: 32 AF XY: 0.000124 AC XY: 9AN XY: 72864
ClinVar
Submissions by phenotype
FOXJ1-related disorder Benign:1
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at