11-755659-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006755.2(TALDO1):​c.98-220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.09 in 611,260 control chromosomes in the GnomAD database, including 2,838 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.077 ( 556 hom., cov: 31)
Exomes 𝑓: 0.094 ( 2282 hom. )

Consequence

TALDO1
NM_006755.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.23
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TALDO1NM_006755.2 linkuse as main transcriptc.98-220G>A intron_variant ENST00000319006.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TALDO1ENST00000319006.8 linkuse as main transcriptc.98-220G>A intron_variant 1 NM_006755.2 P1P37837-1

Frequencies

GnomAD3 genomes
AF:
0.0771
AC:
11725
AN:
152094
Hom.:
558
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0231
Gnomad AMI
AF:
0.0307
Gnomad AMR
AF:
0.0922
Gnomad ASJ
AF:
0.0548
Gnomad EAS
AF:
0.0604
Gnomad SAS
AF:
0.0738
Gnomad FIN
AF:
0.0850
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.109
Gnomad OTH
AF:
0.0718
GnomAD4 exome
AF:
0.0943
AC:
43305
AN:
459048
Hom.:
2282
AF XY:
0.0931
AC XY:
22546
AN XY:
242240
show subpopulations
Gnomad4 AFR exome
AF:
0.0211
Gnomad4 AMR exome
AF:
0.0815
Gnomad4 ASJ exome
AF:
0.0626
Gnomad4 EAS exome
AF:
0.0653
Gnomad4 SAS exome
AF:
0.0714
Gnomad4 FIN exome
AF:
0.0880
Gnomad4 NFE exome
AF:
0.109
Gnomad4 OTH exome
AF:
0.0888
GnomAD4 genome
AF:
0.0771
AC:
11728
AN:
152212
Hom.:
556
Cov.:
31
AF XY:
0.0757
AC XY:
5632
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0230
Gnomad4 AMR
AF:
0.0920
Gnomad4 ASJ
AF:
0.0548
Gnomad4 EAS
AF:
0.0605
Gnomad4 SAS
AF:
0.0731
Gnomad4 FIN
AF:
0.0850
Gnomad4 NFE
AF:
0.109
Gnomad4 OTH
AF:
0.0772
Alfa
AF:
0.0965
Hom.:
1012
Bravo
AF:
0.0738
Asia WGS
AF:
0.0910
AC:
314
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.14
DANN
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3895063; hg19: chr11-755659; API