chr11-749776-C-T

Variant names:

• chr11-749776-C-T
• rs11246300
• NM_006755.2:c.97+2198C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006755.2(TALDO1):​c.97+2198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,220 control chromosomes in the GnomAD database, including 2,545 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 0.16 (2545 hom., cov: 33)
• Consequence: TALDO1 NM_006755.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 20 publications found

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]

TALDO1 Gene-Disease associations (from GenCC):

• transaldolase deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TALDO1	NM_006755.2	c.97+2198C>T		intron_variant	Intron 1 of 7	ENST00000319006.8	NP_006746.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TALDO1	ENST00000319006.8	c.97+2198C>T		intron_variant	Intron 1 of 7	1	NM_006755.2	ENSP00000321259.3

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24431 AN: 152102 Hom.: 2534 Cov.: 33

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0446

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.161 AC: 24452 AN: 152220 Hom.: 2545 Cov.: 33 AF XY: 0.159 AC XY: 11844 AN XY: 74438

African (AFR) AF: 0.0412 AC: 1710 AN: 41546

American (AMR) AF: 0.220 AC: 3363 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 519 AN: 3472

East Asian (EAS) AF: 0.0443 AC: 229 AN: 5172

South Asian (SAS) AF: 0.0927 AC: 448 AN: 4832

European-Finnish (FIN) AF: 0.216 AC: 2290 AN: 10588

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15249 AN: 68008

Other (OTH) AF: 0.162 AC: 342 AN: 2110

Alfa AF: 0.203 Hom.: 3852

Bravo AF: 0.153

Asia WGS AF: 0.0590 AC: 205 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.049
DANN	Benign	0.53
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11246300; hg19: chr11-749776;