NM_001367943.1:c.296C>A

Variant summary

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

The NM_001367943.1(TCF7L2):​c.296C>A​(p.Pro99Gln) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P99L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TCF7L2
NM_001367943.1 missense

Scores

4
7
8

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 4.60
Variant links:
Genes affected
TCF7L2 (HGNC:11641): (transcription factor 7 like 2) This gene encodes a high mobility group (HMG) box-containing transcription factor that plays a key role in the Wnt signaling pathway. The protein has been implicated in blood glucose homeostasis. Genetic variants of this gene are associated with increased risk of type 2 diabetes. Several transcript variants encoding multiple different isoforms have been found for this gene.[provided by RefSeq, Oct 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TCF7L2NM_001367943.1 linkc.296C>A p.Pro99Gln missense_variant Exon 3 of 15 ENST00000355995.9 NP_001354872.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TCF7L2ENST00000355995.9 linkc.296C>A p.Pro99Gln missense_variant Exon 3 of 15 1 NM_001367943.1 ENSP00000348274.4 Q9NQB0-1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1281122
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
637986
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
29

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

TCF7L2-related disorder Uncertain:1
Dec 06, 2023
PreventionGenetics, part of Exact Sciences
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing

The TCF7L2 c.296C>A variant is predicted to result in the amino acid substitution p.Pro99Gln. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.24
BayesDel_addAF
Pathogenic
0.17
D
BayesDel_noAF
Uncertain
0.010
CADD
Uncertain
24
DANN
Uncertain
0.98
DEOGEN2
Benign
0.032
T;T;T;.;T;.;.;.;.;T;.;T;T
Eigen
Benign
-0.23
Eigen_PC
Benign
-0.28
FATHMM_MKL
Benign
0.21
N
LIST_S2
Uncertain
0.96
D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
0.99
D
MetaRNN
Uncertain
0.56
D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Uncertain
2.1
.;.;M;M;.;M;M;M;M;.;.;.;.
PrimateAI
Pathogenic
0.82
D
PROVEAN
Benign
-2.2
N;N;N;N;N;.;N;N;N;D;N;.;D
REVEL
Uncertain
0.56
Sift
Uncertain
0.0060
D;D;D;D;D;.;D;D;D;D;D;.;D
Sift4G
Benign
0.099
T;T;D;T;D;D;T;T;T;T;T;T;D
Polyphen
0.46, 0.25, 0.64
.;P;.;.;.;B;.;.;.;.;P;.;.
Vest4
0.44
MutPred
0.41
Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);Loss of glycosylation at P99 (P = 0.0665);.;
MVP
0.80
MPC
0.58
ClinPred
0.80
D
GERP RS
2.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.26
gMVP
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-114711281; API