rs149911553
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_004817.4(TJP2):āc.1877C>Gā(p.Thr626Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,614,170 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004817.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TJP2 | NM_004817.4 | c.1877C>G | p.Thr626Ser | missense_variant | 13/23 | ENST00000377245.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TJP2 | ENST00000377245.9 | c.1877C>G | p.Thr626Ser | missense_variant | 13/23 | 1 | NM_004817.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00104 AC: 158AN: 152160Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00101 AC: 253AN: 251442Hom.: 0 AF XY: 0.000920 AC XY: 125AN XY: 135892
GnomAD4 exome AF: 0.00138 AC: 2023AN: 1461892Hom.: 2 Cov.: 32 AF XY: 0.00135 AC XY: 982AN XY: 727246
GnomAD4 genome ? AF: 0.00104 AC: 158AN: 152278Hom.: 1 Cov.: 32 AF XY: 0.000900 AC XY: 67AN XY: 74450
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2020 | This variant is associated with the following publications: (PMID: 32089630, 28924228) - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 17, 2014 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 17, 2013 | Thr603Ser in exon 14 of TJP2: This variant is not expected to have clinical sign ificance because it has been identified in 0.2% (14/8600) of European American c hromosomes chromosomes from a broad population by the NHLBI Exome Sequencing Pro ject (http://evs.gs.washington.edu/EVS/; dbSNP rs149911553) and this amino acid position is not evolutionarily conserved in mammals. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at