rs4927602
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000497517.6(TPO):n.66G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,086 control chromosomes in the GnomAD database, including 27,974 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 0.59 ( 27973 hom., cov: 33)
Exomes 𝑓: 0.33 ( 1 hom. )
Consequence
TPO
ENST00000497517.6 non_coding_transcript_exon
ENST00000497517.6 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.239
Genes affected
TPO (HGNC:12015): (thyroid peroxidase) This gene encodes a membrane-bound glycoprotein. The encoded protein acts as an enzyme and plays a central role in thyroid gland function. The protein functions in the iodination of tyrosine residues in thyroglobulin and phenoxy-ester formation between pairs of iodinated tyrosines to generate the thyroid hormones, thyroxine and triiodothyronine. Mutations in this gene are associated with several disorders of thyroid hormonogenesis, including congenital hypothyroidism, congenital goiter, and thyroid hormone organification defect IIA. Multiple transcript variants encoding distinct isoforms have been identified for this gene, but the full-length nature of some variants has not been determined. [provided by RefSeq, May 2011]
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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=-1.0).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPO | XM_024453089.2 | c.-595G>A | 5_prime_UTR_variant | 1/18 | |||
TPO | XM_047445652.1 | c.-1506G>A | 5_prime_UTR_variant | 1/19 | |||
TPO | XM_047445653.1 | c.-691G>A | 5_prime_UTR_variant | 1/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPO | ENST00000497517.6 | n.66G>A | non_coding_transcript_exon_variant | 1/6 | 1 | ||||
ENST00000650512.1 | n.866-6795C>T | intron_variant, non_coding_transcript_variant | |||||||
TPO | ENST00000650224.1 | n.223G>A | non_coding_transcript_exon_variant | 1/4 |
Frequencies
GnomAD3 genomes ? AF: 0.593 AC: 90067AN: 151958Hom.: 27912 Cov.: 33
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GnomAD4 exome AF: 0.333 AC: 4AN: 12Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 4AN XY: 8
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GnomAD4 genome ? AF: 0.593 AC: 90189AN: 152074Hom.: 27973 Cov.: 33 AF XY: 0.593 AC XY: 44064AN XY: 74340
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at