chr1-175354416-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003285.3(TNR):c.3357C>G(p.Ser1119Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1119G) has been classified as Uncertain significance.
Frequency
Consequence
NM_003285.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNR | NM_003285.3 | c.3357C>G | p.Ser1119Arg | missense_variant | 18/23 | ENST00000367674.7 | |
TNR | NM_001328635.2 | c.2358C>G | p.Ser786Arg | missense_variant | 18/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNR | ENST00000367674.7 | c.3357C>G | p.Ser1119Arg | missense_variant | 18/23 | 5 | NM_003285.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Neurodevelopmental disorder, nonprogressive, with spasticity and transient opisthotonus Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Jun 22, 2020 | - - |
Non-progressive neurodevelopmental disorder with spasticity and transient opisthotonus Uncertain:1
Uncertain significance, criteria provided, single submitter | provider interpretation | Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München | Jul 25, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at