rs11107
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PVS1_SupportingBP6_Very_StrongBA1
The NM_001257990.2(FBXO7):c.3G>A(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,613,402 control chromosomes in the GnomAD database, including 136,759 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001257990.2 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBXO7 | NM_012179.4 | c.345G>A | p.Met115Ile | missense_variant | Exon 2 of 9 | ENST00000266087.12 | NP_036311.3 | |
FBXO7 | NM_001257990.2 | c.3G>A | p.Met1? | start_lost | Exon 2 of 9 | NP_001244919.1 | ||
FBXO7 | NM_001033024.2 | c.108G>A | p.Met36Ile | missense_variant | Exon 2 of 9 | NP_001028196.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.416 AC: 63089AN: 151522Hom.: 13628 Cov.: 30
GnomAD3 exomes AF: 0.453 AC: 113761AN: 251364Hom.: 27224 AF XY: 0.447 AC XY: 60780AN XY: 135856
GnomAD4 exome AF: 0.402 AC: 588283AN: 1461758Hom.: 123110 Cov.: 49 AF XY: 0.405 AC XY: 294181AN XY: 727172
GnomAD4 genome AF: 0.416 AC: 63145AN: 151644Hom.: 13649 Cov.: 30 AF XY: 0.425 AC XY: 31503AN XY: 74086
ClinVar
Submissions by phenotype
Parkinsonian-pyramidal syndrome Benign:5
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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
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This variant is associated with the following publications: (PMID: 23222517) -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at