Variant chr11-747445-TCGCCGCCGCCGC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The ENST00000528097.5(TALDO1):c.-30_-19del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00866 in 1,511,000 control chromosomes in the GnomAD database, including 75 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0067 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0089 ( 71 hom. )

Consequence

TALDO1
ENST00000528097.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.357

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-747445-TCGCCGCCGCCGC-T is Benign according to our data. Variant chr11-747445-TCGCCGCCGCCGC-T is described in ClinVar as [Likely_benign]. Clinvar id is 306085.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00675 (1025/151950) while in subpopulation NFE AF= 0.0101 (683/67894). AF 95% confidence interval is 0.00943. There are 4 homozygotes in gnomad4. There are 475 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TALDO1	NM_006755.2 linkuse as main transcript			upstream_gene_variant		ENST00000319006.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TALDO1	ENST00000319006.8 linkuse as main transcript			upstream_gene_variant		1	NM_006755.2	P1	P37837-1

Frequencies

GnomAD3 genomes

AF:

0.00676

AC:

1026

AN:

151844

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00167

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00675

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00694

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.0101

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.00753

AC:

931

AN:

123674

Hom.:

AF XY:

0.00737

AC XY:

509

AN XY:

69020

show subpopulations

Gnomad AFR exome

AF:

0.00119

Gnomad AMR exome

AF:

0.00369

Gnomad ASJ exome

AF:

0.0162

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000631

Gnomad FIN exome

AF:

0.00772

Gnomad NFE exome

AF:

0.0114

Gnomad OTH exome

AF:

0.00972

GnomAD4 exome

AF:

0.00888

AC:

12062

AN:

1359050

Hom.:

AF XY:

0.00862

AC XY:

5801

AN XY:

673052

show subpopulations

Gnomad4 AFR exome

AF:

0.00146

Gnomad4 AMR exome

AF:

0.00404

Gnomad4 ASJ exome

AF:

0.0143

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000536

Gnomad4 FIN exome

AF:

0.00735

Gnomad4 NFE exome

AF:

0.0101

Gnomad4 OTH exome

AF:

0.00809

GnomAD4 genome

AF:

0.00675

AC:

1025

AN:

151950

Hom.:

Cov.:

AF XY:

0.00639

AC XY:

475

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.00674

Gnomad4 ASJ

AF:

0.0156

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00694

Gnomad4 NFE

AF:

0.0101

Gnomad4 OTH

AF:

0.0133

Alfa

AF:

0.00299

Hom.:

Bravo

AF:

0.00651

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Deficiency of transaldolase

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over