chr14-80955802-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PS1_ModeratePP3PP5_Moderate
The NM_000369.5(TSHR):c.122G>C(p.Cys41Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000347 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_000369.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSHR | NM_000369.5 | c.122G>C | p.Cys41Ser | missense_variant | 1/10 | ENST00000298171.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSHR | ENST00000298171.7 | c.122G>C | p.Cys41Ser | missense_variant | 1/10 | 1 | NM_000369.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 249792Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135158
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727236
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
Epilepsy;C0424605:Developmental delay;C1846135:autistic features Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jul 04, 2016 | - - |
Hypothyroidism due to TSH receptor mutations Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2002 | - - |
Familial hyperthyroidism due to mutations in TSH receptor Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2016 | This variant was classified as: Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at