rs185819
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001365276.2(TNXB):c.3482A>T(p.His1161Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 1,600,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/17 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. H1161R) has been classified as Benign.
Frequency
Consequence
NM_001365276.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.3482A>T | p.His1161Leu | missense_variant | 9/44 | ENST00000644971.2 | NP_001352205.1 | |
TNXB | NM_019105.8 | c.3482A>T | p.His1161Leu | missense_variant | 9/44 | NP_061978.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.3482A>T | p.His1161Leu | missense_variant | 9/44 | NM_001365276.2 | ENSP00000496448 | |||
TNXB | ENST00000647633.1 | c.4223A>T | p.His1408Leu | missense_variant | 10/45 | ENSP00000497649 | P1 | |||
TNXB | ENST00000375244.7 | c.3482A>T | p.His1161Leu | missense_variant | 9/44 | 5 | ENSP00000364393 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151668Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000822 AC: 2AN: 243330Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133086
GnomAD4 exome AF: 0.00000483 AC: 7AN: 1448720Hom.: 0 Cov.: 50 AF XY: 0.00000696 AC XY: 5AN XY: 718782
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151668Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74058
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at