10-112293787-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_058222.3(TECTB):c.533C>T(p.Ser178Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000743 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S178S) has been classified as Benign.
Frequency
Consequence
NM_058222.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECTB | ENST00000646139.2 | c.533C>T | p.Ser178Phe | missense_variant | Exon 6 of 11 | NM_058222.3 | ENSP00000494896.1 | |||
TECTB | ENST00000369422.4 | c.533C>T | p.Ser178Phe | missense_variant | Exon 5 of 10 | 1 | ENSP00000358430.3 | |||
TECTB | ENST00000643850.1 | c.563C>T | p.Ser188Phe | missense_variant | Exon 6 of 11 | ENSP00000495832.1 | ||||
TECTB | ENST00000645243.1 | c.533C>T | p.Ser178Phe | missense_variant | Exon 6 of 11 | ENSP00000495514.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251464Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461880Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727242
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.533C>T (p.S178F) alteration is located in exon 5 (coding exon 5) of the TECTB gene. This alteration results from a C to T substitution at nucleotide position 533, causing the serine (S) at amino acid position 178 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at