15-59618818-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004751.3(GCNT3):c.580C>T(p.Arg194Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,038 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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. R194L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004751.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCNT3 | NM_004751.3 | c.580C>T | p.Arg194Trp | missense_variant | Exon 3 of 3 | ENST00000396065.3 | NP_004742.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCNT3 | ENST00000396065.3 | c.580C>T | p.Arg194Trp | missense_variant | Exon 3 of 3 | 1 | NM_004751.3 | ENSP00000379377.1 | ||
GCNT3 | ENST00000560585.5 | c.580C>T | p.Arg194Trp | missense_variant | Exon 3 of 3 | 1 | ENSP00000452741.1 | |||
GCNT3 | ENST00000560210.1 | n.351+1937C>T | intron_variant | Intron 1 of 1 | 3 | |||||
GCNT3 | ENST00000559200.1 | c.*121C>T | downstream_gene_variant | 2 | ENSP00000453774.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152160Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251384Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135844
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461878Hom.: 1 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 727242
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152160Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.580C>T (p.R194W) alteration is located in exon 3 (coding exon 1) of the GCNT3 gene. This alteration results from a C to T substitution at nucleotide position 580, causing the arginine (R) at amino acid position 194 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