rs140222720
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000507.4(FBP1):c.670G>A(p.Val224Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000547 in 1,613,964 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V224V) has been classified as Likely benign.
Frequency
Consequence
NM_000507.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBP1 | NM_000507.4 | c.670G>A | p.Val224Ile | missense_variant | 5/7 | ENST00000375326.9 | |
FBP1 | NM_001127628.2 | c.670G>A | p.Val224Ile | missense_variant | 6/8 | ||
FBP1 | XM_006717005.5 | c.424G>A | p.Val142Ile | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBP1 | ENST00000375326.9 | c.670G>A | p.Val224Ile | missense_variant | 5/7 | 1 | NM_000507.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000388 AC: 59AN: 152212Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000422 AC: 106AN: 251252Hom.: 0 AF XY: 0.000412 AC XY: 56AN XY: 135792
GnomAD4 exome AF: 0.000564 AC: 824AN: 1461634Hom.: 1 Cov.: 42 AF XY: 0.000597 AC XY: 434AN XY: 727130
GnomAD4 genome ? AF: 0.000387 AC: 59AN: 152330Hom.: 0 Cov.: 34 AF XY: 0.000363 AC XY: 27AN XY: 74482
ClinVar
Submissions by phenotype
Fructose-biphosphatase deficiency Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 02, 2014 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at