rs121912575
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001365276.2(TNXB):c.3322G>T(p.Val1108Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,608,674 control chromosomes in the GnomAD database, with no homozygous occurrence. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1108M) has been classified as Likely benign.
Frequency
Consequence
NM_001365276.2 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 |
---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.3322G>T | p.Val1108Leu | missense_variant | 8/44 | ENST00000644971.2 | |
TNXB | NM_019105.8 | c.3322G>T | p.Val1108Leu | missense_variant | 8/44 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.3322G>T | p.Val1108Leu | missense_variant | 8/44 | NM_001365276.2 | |||
TNXB | ENST00000647633.1 | c.4063G>T | p.Val1355Leu | missense_variant | 9/45 | P1 | |||
TNXB | ENST00000375244.7 | c.3322G>T | p.Val1108Leu | missense_variant | 8/44 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456536Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 724360
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at