rs11899823
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_022065.5(THADA):āc.1492T>Cā(p.Leu498=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 1,613,642 control chromosomes in the GnomAD database, including 87,926 homozygotes. 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: š 0.33 ( 8715 hom., cov: 32)
Exomes š: 0.33 ( 79211 hom. )
Consequence
THADA
NM_022065.5 synonymous
NM_022065.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.14
Genes affected
THADA (HGNC:19217): (THADA armadillo repeat containing) This gene is the target of 2p21 choromosomal aberrations in benign thyroid adenomas. Single nucleotide polymorphisms (SNPs) in this gene may be associated with type 2 diabetes and polycystic ovary syndrome. The encoded protein is likely involved in the death receptor pathway and apoptosis. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP7
?
Synonymous conserved (PhyloP=3.14 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THADA | NM_022065.5 | c.1492T>C | p.Leu498= | synonymous_variant | 11/38 | ENST00000405975.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THADA | ENST00000405975.7 | c.1492T>C | p.Leu498= | synonymous_variant | 11/38 | 1 | NM_022065.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.334 AC: 50788AN: 151934Hom.: 8698 Cov.: 32
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GnomAD3 exomes AF: 0.310 AC: 77154AN: 248964Hom.: 12692 AF XY: 0.317 AC XY: 42799AN XY: 135058
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GnomAD4 exome AF: 0.326 AC: 477086AN: 1461590Hom.: 79211 Cov.: 41 AF XY: 0.329 AC XY: 239184AN XY: 727078
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GnomAD4 genome ? AF: 0.334 AC: 50841AN: 152052Hom.: 8715 Cov.: 32 AF XY: 0.331 AC XY: 24606AN XY: 74312
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at