chr10-112950748-G-GA
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 4P and 9B. PVS1_StrongBP6BS1BS2
The NM_001367943.1(TCF7L2):c.1dupA(p.Met1fs) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,533,132 control chromosomes in the GnomAD database, including 61 homozygotes. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001367943.1 frameshift, start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCF7L2 | NM_001367943.1 | c.1dupA | p.Met1fs | frameshift_variant, start_lost | Exon 1 of 15 | ENST00000355995.9 | NP_001354872.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0102 AC: 1528AN: 149780Hom.: 24 Cov.: 29
GnomAD3 exomes AF: 0.00364 AC: 447AN: 122762Hom.: 8 AF XY: 0.00296 AC XY: 194AN XY: 65550
GnomAD4 exome AF: 0.00170 AC: 2348AN: 1383252Hom.: 37 Cov.: 32 AF XY: 0.00161 AC XY: 1096AN XY: 682506
GnomAD4 genome AF: 0.0102 AC: 1529AN: 149880Hom.: 24 Cov.: 29 AF XY: 0.00995 AC XY: 728AN XY: 73134
ClinVar
Submissions by phenotype
TCF7L2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Neoplasm Other:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at