X-123610962-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The NM_001081550.2(THOC2):c.4756C>T(p.His1586Tyr) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,207,680 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001081550.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THOC2 | NM_001081550.2 | c.4756C>T | p.His1586Tyr | missense_variant, splice_region_variant | 38/39 | ENST00000245838.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THOC2 | ENST00000245838.13 | c.4756C>T | p.His1586Tyr | missense_variant, splice_region_variant | 38/39 | 5 | NM_001081550.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111928Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34102
GnomAD3 exomes AF: 0.00000562 AC: 1AN: 178024Hom.: 0 AF XY: 0.0000156 AC XY: 1AN XY: 63976
GnomAD4 exome AF: 0.0000374 AC: 41AN: 1095752Hom.: 0 Cov.: 28 AF XY: 0.0000388 AC XY: 14AN XY: 361234
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111928Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34102
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Aug 08, 2022 | The THOC2 c.4756C>T (p.His1586Tyr) missense variant results in the substitution of histidine at amino acid position 1586 with tyrosine. To our knowledge, this variant has not been reported in the peer-reviewed literature. This variant is reported in the Genome Aggregation Database in two alleles at a frequency of 0.000038 in the European (non-Finnish) population, which includes one hemizygote (version 3.1.2). A second hemizygote is reported in Genome Aggregation Database version 2.1.1. The c.4756C>T variant is located in the RNA binding domain (PMID: 32116545), but the functional impact of the variant is unclear and in silico predictions show mixed results. Based on the available evidence, the c.4756C>T (p.His1586Tyr) variant is classified as a variant of uncertain significance for X-linked intellectual disability-short stature-overweight syndrome. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at