rs397517145
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005422.4(TECTA):c.2199C>G(p.Ser733=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,609,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S733S) has been classified as Likely benign.
Frequency
Consequence
NM_005422.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECTA | NM_005422.4 | c.2199C>G | p.Ser733= | synonymous_variant | 9/24 | ENST00000392793.6 | |
TBCEL-TECTA | NM_001378761.1 | c.3156C>G | p.Ser1052= | synonymous_variant | 15/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECTA | ENST00000392793.6 | c.2199C>G | p.Ser733= | synonymous_variant | 9/24 | 5 | NM_005422.4 | P4 | |
TECTA | ENST00000264037.2 | c.2199C>G | p.Ser733= | synonymous_variant | 8/23 | 1 | P4 | ||
TECTA | ENST00000642222.1 | c.2199C>G | p.Ser733= | synonymous_variant | 9/24 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247398Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134130
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457142Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 2AN XY: 725108
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 05, 2013 | Ser733Ser in TECTA: This variant is not expected to have clinical significance b ecause it does not alter an amino acid residue and is not located within the spl ice consensus sequence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at