rs1555123944
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_005422.4(TECTA):c.1966G>A(p.Gly656Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G656G) has been classified as Likely benign.
Frequency
Consequence
NM_005422.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECTA | NM_005422.4 | c.1966G>A | p.Gly656Ser | missense_variant | 9/24 | ENST00000392793.6 | |
TBCEL-TECTA | NM_001378761.1 | c.2923G>A | p.Gly975Ser | missense_variant | 15/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECTA | ENST00000392793.6 | c.1966G>A | p.Gly656Ser | missense_variant | 9/24 | 5 | NM_005422.4 | P4 | |
TECTA | ENST00000264037.2 | c.1966G>A | p.Gly656Ser | missense_variant | 8/23 | 1 | P4 | ||
TECTA | ENST00000642222.1 | c.1966G>A | p.Gly656Ser | missense_variant | 9/24 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461808Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727212
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 06, 2016 | The p.Gly656Ser variant in TECTA has not been previously reported in individuals with hearing loss or in large population studies. Computational prediction tool s and conservation analysis do not provide strong support for or against an impa ct to the protein. In summary, the clinical significance of the p.Gly656Ser vari ant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at