chr8-142300512-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_145003.5(TSNARE1):c.1264C>T(p.Arg422Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,607,608 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_145003.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSNARE1 | NM_145003.5 | c.1264C>T | p.Arg422Trp | missense_variant | 10/14 | ENST00000524325.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSNARE1 | ENST00000524325.6 | c.1264C>T | p.Arg422Trp | missense_variant | 10/14 | 2 | NM_145003.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000932 AC: 23AN: 246796Hom.: 0 AF XY: 0.0000747 AC XY: 10AN XY: 133788
GnomAD4 exome AF: 0.0000295 AC: 43AN: 1455338Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 724122
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152270Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 2023 | The c.1264C>T (p.R422W) alteration is located in exon 10 (coding exon 9) of the TSNARE1 gene. This alteration results from a C to T substitution at nucleotide position 1264, causing the arginine (R) at amino acid position 422 to be replaced by a tryptophan (W). 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