rs886048658

Variant names:

• chr11-747529-C-G
• rs886048658
• NM_006755.2:c.48C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-747529-C-G
• chr11-747529-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_006755.2(TALDO1):​c.48C>G​(p.Asp16Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. D16D) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: TALDO1 NM_006755.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16070712).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TALDO1	NM_006755.2	c.48C>G	p.Asp16Glu	missense_variant	Exon 1 of 8	ENST00000319006.8	NP_006746.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TALDO1	ENST00000319006.8	c.48C>G	p.Asp16Glu	missense_variant	Exon 1 of 8	1	NM_006755.2	ENSP00000321259.3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 34

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.74
DEOGEN2	Benign	0.33	T;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.61	D
LIST_S2	Benign	0.81	T;T
M_CAP	Pathogenic	0.67	D
MetaRNN	Benign	0.16	T;T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	-0.52	N;.
PrimateAI	Pathogenic	0.85	D
PROVEAN	Benign	-0.14	N;N
REVEL	Benign	0.22
Sift	Benign	0.84	T;T
Sift4G	Benign	1.0	T;T
Polyphen		0.0	B;B
Vest4		0.048
MutPred		0.39		Gain of ubiquitination at K19 (P = 0.0685);Gain of ubiquitination at K19 (P = 0.0685);
MVP		0.53
MPC		0.067
ClinPred		0.035	T
GERP RS		-4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.057
gMVP		0.28

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: rs886048658; hg19: chr11-747529;