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rs7903146

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5BP4

The NM_001367943.1(TCF7L2):c.450+33966C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely risk allele (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

TCF7L2
NM_001367943.1 intron

Scores

2

Clinical Significance

Likely risk allele no assertion criteria provided P:1

Conservation

PhyloP100: 0.133
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.

PP5
Variant 10-112998590-C-G is Pathogenic according to our data. Variant chr10-112998590-C-G is described in ClinVar as [Likely_risk_allele]. Clinvar id is 1692994.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_pathogenic, oryginal submission is: [Likely_risk_allele].
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TCF7L2NM_001367943.1 linkuse as main transcriptc.450+33966C>G intron_variant ENST00000355995.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TCF7L2ENST00000355995.9 linkuse as main transcriptc.450+33966C>G intron_variant 1 NM_001367943.1 Q9NQB0-1

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Likely risk allele
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Type 2 diabetes mellitus Pathogenic:1
Likely risk allele, no assertion criteria providedreference populationiDNA GenomicsJan 09, 2011- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
3.0
Dann
Benign
0.33

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

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

Other links and lift over

dbSNP: rs7903146; hg19: chr10-114758349; API