rs3895063

Variant names:

• chr11-755659-G-A
• rs3895063
• NM_006755.2:c.98-220G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-755659-G-A
• chr11-755659-G-T

Variant summary

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

The ENST00000319006.8(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 ENST00000319006.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000319006.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TALDO1	NM_006755.2	MANE Select	c.98-220G>A		intron	N/A	NP_006746.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TALDO1	ENST00000319006.8	TSL:1 MANE Select	c.98-220G>A		intron	N/A	ENSP00000321259.3
	TALDO1	ENST00000528097.5	TSL:1	c.98-220G>A		intron	N/A	ENSP00000437098.1
	TALDO1	ENST00000528070.5	TSL:5	n.*155-220G>A		intron	N/A	ENSP00000435042.1

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

African (AFR) AF: 0.0211 AC: 277 AN: 13156

American (AMR) AF: 0.0815 AC: 2027 AN: 24878

Ashkenazi Jewish (ASJ) AF: 0.0626 AC: 876 AN: 13992

East Asian (EAS) AF: 0.0653 AC: 1814 AN: 27800

South Asian (SAS) AF: 0.0714 AC: 3551 AN: 49742

European-Finnish (FIN) AF: 0.0880 AC: 2213 AN: 25146

Middle Eastern (MID) AF: 0.0483 AC: 93 AN: 1926

European-Non Finnish (NFE) AF: 0.109 AC: 30194 AN: 276948

Other (OTH) AF: 0.0888 AC: 2260 AN: 25460

GnomAD4 genome AF: 0.0771 AC: 11728 AN: 152212 Hom.: 556 Cov.: 31 AF XY: 0.0757 AC XY: 5632 AN XY: 74408

African (AFR) AF: 0.0230 AC: 956 AN: 41556

American (AMR) AF: 0.0920 AC: 1405 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3468

East Asian (EAS) AF: 0.0605 AC: 314 AN: 5188

South Asian (SAS) AF: 0.0731 AC: 352 AN: 4818

European-Finnish (FIN) AF: 0.0850 AC: 899 AN: 10582

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7412 AN: 68004

Other (OTH) AF: 0.0772 AC: 163 AN: 2112

Alfa AF: 0.0951 Hom.: 1323

Bravo AF: 0.0738

Asia WGS AF: 0.0910 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.58
PhyloP100		-2.2
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: rs3895063; hg19: chr11-755659;