17-40062520-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000578218.5(THRA):c.-326G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,884 control chromosomes in the GnomAD database, including 11,305 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: 𝑓 0.38 ( 11303 hom., cov: 30)
Exomes 𝑓: 0.39 ( 2 hom. )
Consequence
THRA
ENST00000578218.5 5_prime_UTR
ENST00000578218.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.81
Genes affected
THRA (HGNC:11796): (thyroid hormone receptor alpha) The protein encoded by this gene is a nuclear hormone receptor for triiodothyronine. It is one of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone. Knockout studies in mice suggest that the different receptors, while having certain extent of redundancy, may mediate different functions of thyroid hormone. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THRA | NM_001190919.2 | c.-298+69G>A | intron_variant | NP_001177848.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THRA | ENST00000578218.5 | c.-326G>A | 5_prime_UTR_variant | 1/5 | 4 | ENSP00000464123 | ||||
THRA | ENST00000394121.8 | c.-298+69G>A | intron_variant | 2 | ENSP00000377679 | |||||
THRA | ENST00000577288.5 | c.-298+4042G>A | intron_variant | 4 | ENSP00000464013 | |||||
THRA | ENST00000585047.5 | c.-298+558G>A | intron_variant | 4 | ENSP00000462955 |
Frequencies
GnomAD3 genomes AF: 0.377 AC: 57130AN: 151738Hom.: 11284 Cov.: 30
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GnomAD4 exome AF: 0.393 AC: 11AN: 28Hom.: 2 Cov.: 0 AF XY: 0.450 AC XY: 9AN XY: 20
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GnomAD4 genome AF: 0.377 AC: 57181AN: 151856Hom.: 11303 Cov.: 30 AF XY: 0.377 AC XY: 27956AN XY: 74178
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at