10-112950449-GTTTT-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001367943.1(TCF7L2):c.-297_-294delTTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 195,186 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0017 ( 2 hom., cov: 17)
Exomes 𝑓: 0.00032 ( 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: 1.60
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 Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00172 (207/120642) while in subpopulation AMR AF= 0.0177 (203/11440). AF 95% confidence interval is 0.0157. There are 2 homozygotes in gnomad4. There are 140 alleles in male gnomad4 subpopulation. Median coverage is 17. This position pass quality control queck.
BS2
High AC in GnomAd4 at 207 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCF7L2 | NM_001367943.1 | c.-297_-294delTTTT | 5_prime_UTR_variant | Exon 1 of 15 | ENST00000355995.9 | NP_001354872.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00172 AC: 207AN: 120632Hom.: 2 Cov.: 17
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GnomAD4 exome AF: 0.000322 AC: 24AN: 74544Hom.: 0 AF XY: 0.000215 AC XY: 8AN XY: 37228
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GnomAD4 genome AF: 0.00172 AC: 207AN: 120642Hom.: 2 Cov.: 17 AF XY: 0.00246 AC XY: 140AN XY: 56922
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at