rs2297084
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000507.4(FBP1):c.705+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,610,456 control chromosomes in the GnomAD database, including 206,952 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000507.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBP1 | NM_000507.4 | c.705+14C>T | intron_variant | Intron 5 of 6 | ENST00000375326.9 | NP_000498.2 | ||
FBP1 | NM_001127628.2 | c.705+14C>T | intron_variant | Intron 6 of 7 | NP_001121100.1 | |||
FBP1 | XM_006717005.5 | c.459+14C>T | intron_variant | Intron 5 of 6 | XP_006717068.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.509 AC: 77319AN: 151950Hom.: 19854 Cov.: 33
GnomAD3 exomes AF: 0.517 AC: 127174AN: 246200Hom.: 33936 AF XY: 0.511 AC XY: 68031AN XY: 133212
GnomAD4 exome AF: 0.503 AC: 733738AN: 1458388Hom.: 187083 Cov.: 39 AF XY: 0.501 AC XY: 363778AN XY: 725448
GnomAD4 genome AF: 0.509 AC: 77376AN: 152068Hom.: 19869 Cov.: 33 AF XY: 0.506 AC XY: 37575AN XY: 74324
ClinVar
Submissions by phenotype
Fructose-biphosphatase deficiency Benign:3
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. -
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not provided Benign:2
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at