rs3901233

Positions:

• chr11-749452-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006755.2(TALDO1):​c.97+1874T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 149,866 control chromosomes in the GnomAD database, including 13,420 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 0.40 (13420 hom., cov: 30)
• Consequence: TALDO1 NM_006755.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TALDO1	NM_006755.2	c.97+1874T>A		intron_variant		ENST00000319006.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TALDO1	ENST00000319006.8	c.97+1874T>A		intron_variant		1	NM_006755.2	P1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 60454 AN: 149754 Hom.: 13408 Cov.: 30

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.419

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.400

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.404 AC: 60490 AN: 149866 Hom.: 13420 Cov.: 30 AF XY: 0.399 AC XY: 29059 AN XY: 72744

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.399

Alfa AF: 0.460 Hom.: 2130

Bravo AF: 0.403

Asia WGS AF: 0.267 AC: 930 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.13

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

Other links and lift over

dbSNP: rs3901233; hg19: chr11-749452;