rs4506565
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001367943(TCF7L2):c.450+31658A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000395 in 151992 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Consequence
TCF7L2
NM_001367943 intron
NM_001367943 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.773
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| TCF7L2 | NM_001367943.1 | c.450+31658A>G | intron_variant | ENST00000355995.9 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TCF7L2 | ENST00000355995.9 | c.450+31658A>G | intron_variant | 1 | NM_001367943.1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151992Hom.: 0 Cov.: 32
GnomAD3 genomes
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AC:
6
AN:
151992
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Cov.:
32
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at