2-113216028-T-TTA
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_003466.4(PAX8):c.*2503_*2504dupTA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 210,604 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
PAX8
NM_003466.4 3_prime_UTR
NM_003466.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.332
Genes affected
PAX8 (HGNC:8622): (paired box 8) This gene encodes a member of the paired box (PAX) family of transcription factors. Members of this gene family typically encode proteins that contain a paired box domain, an octapeptide, and a paired-type homeodomain. This nuclear protein is involved in thyroid follicular cell development and expression of thyroid-specific genes. Mutations in this gene have been associated with thyroid dysgenesis, thyroid follicular carcinomas and atypical follicular thyroid adenomas. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000125 (19/152150) while in subpopulation AMR AF= 0.000458 (7/15296). AF 95% confidence interval is 0.000215. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High AC in GnomAd4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PAX8 | NM_003466.4 | c.*2503_*2504dupTA | 3_prime_UTR_variant | 12/12 | ENST00000429538.8 | NP_003457.1 | ||
PAX8 | NM_013952.4 | c.*2580_*2581dupTA | 3_prime_UTR_variant | 12/12 | NP_039246.1 | |||
PAX8 | NM_013953.4 | c.*2580_*2581dupTA | 3_prime_UTR_variant | 10/10 | NP_039247.1 | |||
PAX8 | NM_013992.4 | c.*2580_*2581dupTA | 3_prime_UTR_variant | 9/9 | NP_054698.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PAX8 | ENST00000429538 | c.*2503_*2504dupTA | 3_prime_UTR_variant | 12/12 | 1 | NM_003466.4 | ENSP00000395498.3 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152030Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000103 AC: 6AN: 58454Hom.: 0 Cov.: 0 AF XY: 0.000112 AC XY: 3AN XY: 26850
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74378
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital hypothyroidism Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at