chr9-94603132-CT-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000507.4(FBP1):c.*248del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.51 ( 20117 hom., cov: 0)
Exomes 𝑓: 0.50 ( 49360 hom. )
Consequence
FBP1
NM_000507.4 3_prime_UTR
NM_000507.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.192
Genes affected
FBP1 (HGNC:3606): (fructose-bisphosphatase 1) Fructose-1,6-bisphosphatase 1, a gluconeogenesis regulatory enzyme, catalyzes the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate and inorganic phosphate. Fructose-1,6-diphosphatase deficiency is associated with hypoglycemia and metabolic acidosis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 9-94603132-CT-C is Benign according to our data. Variant chr9-94603132-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 367554.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBP1 | NM_000507.4 | c.*248del | 3_prime_UTR_variant | 7/7 | ENST00000375326.9 | ||
FBP1 | NM_001127628.2 | c.*248del | 3_prime_UTR_variant | 8/8 | |||
FBP1 | XM_006717005.5 | c.*248del | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBP1 | ENST00000375326.9 | c.*248del | 3_prime_UTR_variant | 7/7 | 1 | NM_000507.4 | P1 | ||
PCAT7 | ENST00000647389.1 | n.1642-150del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.512 AC: 77796AN: 151808Hom.: 20103 Cov.: 0
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GnomAD4 exome AF: 0.499 AC: 191428AN: 383548Hom.: 49360 Cov.: 0 AF XY: 0.496 AC XY: 100053AN XY: 201860
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GnomAD4 genome ? AF: 0.512 AC: 77852AN: 151926Hom.: 20117 Cov.: 0 AF XY: 0.509 AC XY: 37776AN XY: 74236
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 29, 2018 | - - |
Fructose-biphosphatase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at