rs3895063

chr11-755659-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

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=-0.91).
• 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
TALDO1	NM_006755.2	c.98-220G>A		intron_variant		ENST00000319006.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TALDO1	ENST00000319006.8	c.98-220G>A		intron_variant		1	NM_006755.2	P1

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11725 AN: 152094 Hom.: 558 Cov.: 31

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

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

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

Other links and lift over

dbSNP: rs3895063; hg19: chr11-755659;