rs192327462
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_012179.4(FBXO7):c.122+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00546 in 1,540,668 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012179.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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FBXO7 | NM_012179.4 | c.122+9G>A | intron_variant | Intron 1 of 8 | ENST00000266087.12 | NP_036311.3 | ||
FBXO7 | NM_001033024.2 | c.-229G>A | upstream_gene_variant | NP_001028196.1 | ||||
FBXO7 | NM_001257990.2 | c.-486G>A | upstream_gene_variant | NP_001244919.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00394 AC: 599AN: 152210Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00311 AC: 425AN: 136722Hom.: 0 AF XY: 0.00308 AC XY: 228AN XY: 74050
GnomAD4 exome AF: 0.00563 AC: 7820AN: 1388350Hom.: 25 Cov.: 32 AF XY: 0.00546 AC XY: 3736AN XY: 684556
GnomAD4 genome AF: 0.00393 AC: 598AN: 152318Hom.: 3 Cov.: 33 AF XY: 0.00349 AC XY: 260AN XY: 74474
ClinVar
Submissions by phenotype
Parkinsonian-pyramidal syndrome Uncertain:1Benign:3
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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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
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not specified Benign:1
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not provided Benign:1
FBXO7: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at