chr14-91802295-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001128596.3(TC2N):c.428G>A(p.Arg143His) variant causes a missense change. The variant allele was found at a frequency of 0.0000025 in 1,601,890 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R143C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001128596.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TC2N | NM_001128596.3 | c.428G>A | p.Arg143His | missense_variant | 4/12 | ENST00000435962.7 | |
TC2N | NM_001128595.3 | c.428G>A | p.Arg143His | missense_variant | 4/12 | ||
TC2N | NM_152332.6 | c.428G>A | p.Arg143His | missense_variant | 4/12 | ||
TC2N | NM_001289134.2 | c.428G>A | p.Arg143His | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TC2N | ENST00000435962.7 | c.428G>A | p.Arg143His | missense_variant | 4/12 | 2 | NM_001128596.3 | P1 | |
TC2N | ENST00000340892.9 | c.428G>A | p.Arg143His | missense_variant | 4/12 | 1 | P1 | ||
TC2N | ENST00000360594.9 | c.428G>A | p.Arg143His | missense_variant | 4/12 | 1 | P1 | ||
TC2N | ENST00000556018.5 | c.428G>A | p.Arg143His | missense_variant | 4/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1449792Hom.: 0 Cov.: 34 AF XY: 0.00000139 AC XY: 1AN XY: 720846
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.428G>A (p.R143H) alteration is located in exon 4 (coding exon 3) of the TC2N gene. This alteration results from a G to A substitution at nucleotide position 428, causing the arginine (R) at amino acid position 143 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at