22-32491163-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_012179.4(FBXO7):c.949C>T(p.Leu317Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 1,606,990 control chromosomes in the GnomAD database, including 136,332 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_012179.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBXO7 | NM_012179.4 | c.949C>T | p.Leu317Leu | synonymous_variant | Exon 6 of 9 | ENST00000266087.12 | NP_036311.3 | |
FBXO7 | NM_001033024.2 | c.712C>T | p.Leu238Leu | synonymous_variant | Exon 6 of 9 | NP_001028196.1 | ||
FBXO7 | NM_001257990.2 | c.607C>T | p.Leu203Leu | synonymous_variant | Exon 6 of 9 | NP_001244919.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.416 AC: 63190AN: 151768Hom.: 13645 Cov.: 31
GnomAD3 exomes AF: 0.453 AC: 113653AN: 251146Hom.: 27194 AF XY: 0.447 AC XY: 60736AN XY: 135758
GnomAD4 exome AF: 0.402 AC: 584951AN: 1455106Hom.: 122668 Cov.: 30 AF XY: 0.404 AC XY: 292696AN XY: 724178
GnomAD4 genome AF: 0.416 AC: 63241AN: 151884Hom.: 13664 Cov.: 31 AF XY: 0.426 AC XY: 31578AN XY: 74196
ClinVar
Submissions by phenotype
Parkinsonian-pyramidal syndrome Benign:5
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
- -
- -
- -
- -
not provided Benign:2
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at