chr14-81108501-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000554263.5(TSHR):c.*45T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.02 in 1,505,526 control chromosomes in the GnomAD database, including 521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000554263.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSHR | NM_000369.5 | c.692+49T>C | intron_variant | Intron 8 of 9 | ENST00000298171.7 | NP_000360.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSHR | ENST00000298171.7 | c.692+49T>C | intron_variant | Intron 8 of 9 | 1 | NM_000369.5 | ENSP00000298171.2 |
Frequencies
GnomAD3 genomes AF: 0.0143 AC: 2088AN: 146018Hom.: 26 Cov.: 25
GnomAD4 exome AF: 0.0206 AC: 28014AN: 1359460Hom.: 495 Cov.: 34 AF XY: 0.0202 AC XY: 13676AN XY: 676716
GnomAD4 genome AF: 0.0143 AC: 2088AN: 146066Hom.: 26 Cov.: 25 AF XY: 0.0136 AC XY: 966AN XY: 70800
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: classification based on high MAF (>1% in 1000Genomes), outside of splice consensus sequence and lack of conservation -
Familial gestational hyperthyroidism Benign:1
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Hypothyroidism due to TSH receptor mutations Benign:1
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not provided Benign:1
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Familial hyperthyroidism due to mutations in TSH receptor Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at