rs8192689
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000507.4(FBP1):c.426+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 1,590,510 control chromosomes in the GnomAD database, including 95,582 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000507.4 splice_region, 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBP1 | NM_000507.4 | c.426+7C>T | splice_region_variant, intron_variant | ENST00000375326.9 | |||
FBP1 | NM_001127628.2 | c.426+7C>T | splice_region_variant, intron_variant | ||||
FBP1 | XM_006717005.5 | c.180+7C>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBP1 | ENST00000375326.9 | c.426+7C>T | splice_region_variant, intron_variant | 1 | NM_000507.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.321 AC: 48755AN: 151770Hom.: 7978 Cov.: 32
GnomAD3 exomes AF: 0.336 AC: 84275AN: 250660Hom.: 15330 AF XY: 0.341 AC XY: 46165AN XY: 135500
GnomAD4 exome AF: 0.343 AC: 492730AN: 1438622Hom.: 87593 Cov.: 29 AF XY: 0.344 AC XY: 246727AN XY: 717162
GnomAD4 genome ? AF: 0.321 AC: 48804AN: 151888Hom.: 7989 Cov.: 32 AF XY: 0.322 AC XY: 23877AN XY: 74226
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 30, 2012 | - - |
Fructose-biphosphatase deficiency Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 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:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at