chr11-763998-G-C

Position:

• chr11-763998-G-C

Variant summary

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

The NM_006755.2(TALDO1):​c.835+54G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,579,332 control chromosomes in the GnomAD database, including 44,701 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 0.28 (7411 hom., cov: 33)
  • Exomes 𝑓: 0.22 (37290 hom.)
• Consequence: TALDO1 NM_006755.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TALDO1	NM_006755.2	c.835+54G>C		intron_variant		ENST00000319006.8	NP_006746.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TALDO1	ENST00000319006.8	c.835+54G>C		intron_variant		1	NM_006755.2	ENSP00000321259.3
TALDO1	ENST00000528097.5	c.831+58G>C		intron_variant		1		ENSP00000437098.1
TALDO1	ENST00000530666.1	n.17G>C		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43075 AN: 152086 Hom.: 7402 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.249

GnomAD4 exome AF: 0.221 AC: 315582 AN: 1427128 Hom.: 37290 Cov.: 31 AF XY: 0.218 AC XY: 154378 AN XY: 709514

Gnomad4 AFR exome AF: 0.494

Gnomad4 AMR exome AF: 0.149

Gnomad4 ASJ exome AF: 0.120

Gnomad4 EAS exome AF: 0.0958

Gnomad4 SAS exome AF: 0.138

Gnomad4 FIN exome AF: 0.228

Gnomad4 NFE exome AF: 0.229

Gnomad4 OTH exome AF: 0.219

GnomAD4 genome AF: 0.283 AC: 43109 AN: 152204 Hom.: 7411 Cov.: 33 AF XY: 0.278 AC XY: 20660 AN XY: 74430

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.253

Alfa AF: 0.130 Hom.: 228

Bravo AF: 0.289

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3891028; hg19: chr11-763998;