12-104757039-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018413.6(CHST11):c.295C>T(p.Arg99Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,613,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018413.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.295C>T | p.Arg99Trp | missense_variant | Exon 3 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.280C>T | p.Arg94Trp | missense_variant | Exon 3 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.58C>T | p.Arg20Trp | missense_variant | Exon 2 of 2 | XP_047284870.1 | ||
CHST11 | XM_047428915.1 | c.58C>T | p.Arg20Trp | missense_variant | Exon 2 of 2 | XP_047284871.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST11 | ENST00000303694.6 | c.295C>T | p.Arg99Trp | missense_variant | Exon 3 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
CHST11 | ENST00000549260.5 | c.280C>T | p.Arg94Trp | missense_variant | Exon 3 of 3 | 1 | ENSP00000450004.1 | |||
CHST11 | ENST00000549016.1 | c.175C>T | p.Arg59Trp | missense_variant | Exon 3 of 3 | 4 | ENSP00000449095.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250770Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135770
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461828Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727214
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.295C>T (p.R99W) alteration is located in exon 3 (coding exon 3) of the CHST11 gene. This alteration results from a C to T substitution at nucleotide position 295, causing the arginine (R) at amino acid position 99 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