10-112298073-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_058222.3(TECTB):c.676C>A(p.Pro226Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_058222.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECTB | ENST00000646139.2 | c.676C>A | p.Pro226Thr | missense_variant | Exon 8 of 11 | NM_058222.3 | ENSP00000494896.1 | |||
TECTB | ENST00000369422.4 | c.676C>A | p.Pro226Thr | missense_variant | Exon 7 of 10 | 1 | ENSP00000358430.3 | |||
TECTB | ENST00000643850.1 | c.706C>A | p.Pro236Thr | missense_variant | Exon 8 of 11 | ENSP00000495832.1 | ||||
TECTB | ENST00000645243.1 | c.676C>A | p.Pro226Thr | missense_variant | Exon 8 of 11 | ENSP00000495514.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251394Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135864
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727226
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.676C>A (p.P226T) alteration is located in exon 7 (coding exon 7) of the TECTB gene. This alteration results from a C to A substitution at nucleotide position 676, causing the proline (P) at amino acid position 226 to be replaced by a threonine (T). 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