10-112950449-GTTTT-GTTTTTTT
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001367943.1(TCF7L2):c.-296_-294dupTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000017 ( 0 hom., cov: 17)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
TCF7L2
NM_001367943.1 5_prime_UTR
NM_001367943.1 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.385
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 Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCF7L2 | NM_001367943.1 | c.-296_-294dupTTT | 5_prime_UTR_variant | Exon 1 of 15 | ENST00000355995.9 | NP_001354872.1 |
Ensembl
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GnomAD3 genomes AF: 0.0000249 AC: 3AN: 120628Hom.: 0 Cov.: 17
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GnomAD4 exome AF: 0.000174 AC: 13AN: 74536Hom.: 0 Cov.: 0 AF XY: 0.000161 AC XY: 6AN XY: 37226
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GnomAD4 genome AF: 0.0000166 AC: 2AN: 120638Hom.: 0 Cov.: 17 AF XY: 0.0000351 AC XY: 2AN XY: 56920
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Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at