chr10-112284525-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_058222.3(TECTB):c.77-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,594,504 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_058222.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TECTB | ENST00000646139.2 | c.77-10C>T | intron_variant | Intron 2 of 10 | NM_058222.3 | ENSP00000494896.1 | ||||
TECTB | ENST00000369422.4 | c.77-10C>T | intron_variant | Intron 1 of 9 | 1 | ENSP00000358430.3 | ||||
TECTB | ENST00000643850.1 | c.77-10C>T | intron_variant | Intron 2 of 10 | ENSP00000495832.1 | |||||
TECTB | ENST00000645243.1 | c.77-10C>T | intron_variant | Intron 2 of 10 | ENSP00000495514.1 |
Frequencies
GnomAD3 genomes AF: 0.00277 AC: 421AN: 152176Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000862 AC: 207AN: 240098Hom.: 0 AF XY: 0.000680 AC XY: 88AN XY: 129344
GnomAD4 exome AF: 0.000331 AC: 477AN: 1442210Hom.: 3 Cov.: 30 AF XY: 0.000299 AC XY: 214AN XY: 715092
GnomAD4 genome AF: 0.00276 AC: 421AN: 152294Hom.: 1 Cov.: 33 AF XY: 0.00286 AC XY: 213AN XY: 74462
ClinVar
Submissions by phenotype
TECTB-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at