11-747445-TCGCCGCCGCCGC-TCGCCGCCGCCGCCGCCGC

Variant names:

• chr11-747445-T-TCGCCGC
• rs71464113
• ENST00000319006:c.-24_-19dupCGCCGC

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The ENST00000319006(TALDO1):​c.-24_-19dupCGCCGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00027 in 1,511,082 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00051 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00024 (0 hom.)
• Consequence: TALDO1 ENST00000319006 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000507 (77/151950) while in subpopulation AFR AF= 0.000988 (41/41508). AF 95% confidence interval is 0.000748. There are 0 homozygotes in gnomad4. There are 31 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TALDO1	NM_006755.2	c.-37_-36insCGCCGC		upstream_gene_variant		ENST00000319006.8	NP_006746.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TALDO1	ENST00000319006	c.-24_-19dupCGCCGC		5_prime_UTR_variant	Exon 1 of 8	1	NM_006755.2	ENSP00000321259.3
TALDO1	ENST00000319006.8	c.-37_-36insCGCCGC		upstream_gene_variant		1	NM_006755.2	ENSP00000321259.3

Frequencies

GnomAD3 genomes AF: 0.000501 AC: 76 AN: 151844 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000991

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000236

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.000332 AC: 41 AN: 123674 Hom.: 0 AF XY: 0.000420 AC XY: 29 AN XY: 69020

Gnomad AFR exome AF: 0.000896

Gnomad AMR exome AF: 0.000104

Gnomad ASJ exome AF: 0.00322

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000368

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000115

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000244 AC: 331 AN: 1359132 Hom.: 0 Cov.: 25 AF XY: 0.000273 AC XY: 184 AN XY: 673092

Gnomad4 AFR exome AF: 0.00150

Gnomad4 AMR exome AF: 0.0000599

Gnomad4 ASJ exome AF: 0.00284

Gnomad4 EAS exome AF: 0.000128

Gnomad4 SAS exome AF: 0.000353

Gnomad4 FIN exome AF: 0.0000211

Gnomad4 NFE exome AF: 0.000142

Gnomad4 OTH exome AF: 0.000623

GnomAD4 genome AF: 0.000507 AC: 77 AN: 151950 Hom.: 0 Cov.: 33 AF XY: 0.000417 AC XY: 31 AN XY: 74280

Gnomad4 AFR AF: 0.000988

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000250

Gnomad4 OTH AF: 0.00237

Bravo AF: 0.000582

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71464113; hg19: chr11-747445;