rs7933290
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The 11-765037-G-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00587 in 707,282 control chromosomes in the GnomAD database, including 116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.018 ( 76 hom., cov: 33)
Exomes 𝑓: 0.0026 ( 40 hom. )
Consequence
TALDO1
NM_006755.2 downstream_gene
NM_006755.2 downstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.39
Genes affected
TALDO1 (HGNC:11559): (transaldolase 1) Transaldolase 1 is a key enzyme of the nonoxidative pentose phosphate pathway providing ribose-5-phosphate for nucleic acid synthesis and NADPH for lipid biosynthesis. This pathway can also maintain glutathione at a reduced state and thus protect sulfhydryl groups and cellular integrity from oxygen radicals. The functional gene of transaldolase 1 is located on chromosome 11 and a pseudogene is identified on chromosome 1 but there are conflicting map locations. The second and third exon of this gene were developed by insertion of a retrotransposable element. This gene is thought to be involved in multiple sclerosis. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 11-765037-G-A is Benign according to our data. Variant chr11-765037-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 368974.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TALDO1 | NM_006755.2 | downstream_gene_variant | ENST00000319006.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TALDO1 | ENST00000319006.8 | downstream_gene_variant | 1 | NM_006755.2 | P1 | ||||
TALDO1 | ENST00000528097.5 | downstream_gene_variant | 1 | ||||||
TALDO1 | ENST00000532202.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0178 AC: 2704AN: 152092Hom.: 74 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
2704
AN:
152092
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00258 AC: 1434AN: 555072Hom.: 40 Cov.: 7 AF XY: 0.00217 AC XY: 640AN XY: 294760
GnomAD4 exome
AF:
AC:
1434
AN:
555072
Hom.:
Cov.:
7
AF XY:
AC XY:
640
AN XY:
294760
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0179 AC: 2717AN: 152210Hom.: 76 Cov.: 33 AF XY: 0.0174 AC XY: 1297AN XY: 74402
GnomAD4 genome
?
AF:
AC:
2717
AN:
152210
Hom.:
Cov.:
33
AF XY:
AC XY:
1297
AN XY:
74402
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
10
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Deficiency of transaldolase Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at