rs10849033

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000635110.1(TIGAR):​c.-146+7200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,228 control chromosomes in the GnomAD database, including 55,595 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 0.83 ( 55595 hom., cov: 34)

Consequence

TIGAR
ENST00000635110.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.713
Variant links:
Genes affected
TIGAR (HGNC:1185): (TP53 induced glycolysis regulatory phosphatase) This gene is regulated as part of the p53 tumor suppressor pathway and encodes a protein with sequence similarity to the bisphosphate domain of the glycolytic enzyme that degrades fructose-2,6-bisphosphate. The protein functions by blocking glycolysis and directing the pathway into the pentose phosphate shunt. Expression of this protein also protects cells from DNA damaging reactive oxygen species and provides some protection from DNA damage-induced apoptosis. The 12p13.32 region that includes this gene is paralogous to the 11q13.3 region. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TIGARENST00000635110.1 linkuse as main transcriptc.-146+7200G>A intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.835
AC:
126960
AN:
152110
Hom.:
55605
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.580
Gnomad AMI
AF:
0.985
Gnomad AMR
AF:
0.827
Gnomad ASJ
AF:
0.973
Gnomad EAS
AF:
0.528
Gnomad SAS
AF:
0.864
Gnomad FIN
AF:
0.957
Gnomad MID
AF:
0.953
Gnomad NFE
AF:
0.983
Gnomad OTH
AF:
0.857
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.834
AC:
126981
AN:
152228
Hom.:
55595
Cov.:
34
AF XY:
0.831
AC XY:
61870
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.579
Gnomad4 AMR
AF:
0.826
Gnomad4 ASJ
AF:
0.973
Gnomad4 EAS
AF:
0.527
Gnomad4 SAS
AF:
0.865
Gnomad4 FIN
AF:
0.957
Gnomad4 NFE
AF:
0.983
Gnomad4 OTH
AF:
0.853
Alfa
AF:
0.941
Hom.:
96056
Bravo
AF:
0.810
Asia WGS
AF:
0.677
AC:
2357
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.5
DANN
Benign
0.58

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.

Other links and lift over

dbSNP: rs10849033; hg19: chr12-4425122; API