12-104601911-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018413.6(CHST11):c.124C>T(p.Arg42Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000223 in 1,613,048 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.124C>T | p.Arg42Trp | missense_variant | Exon 2 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.109C>T | p.Arg37Trp | missense_variant | Exon 2 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.-34+144382C>T | intron_variant | Intron 1 of 1 | XP_047284870.1 | |||
CHST11 | XM_047428915.1 | c.-34+144397C>T | intron_variant | Intron 1 of 1 | XP_047284871.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250966Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135654
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460860Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 726800
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.124C>T (p.R42W) alteration is located in exon 2 (coding exon 2) of the CHST11 gene. This alteration results from a C to T substitution at nucleotide position 124, causing the arginine (R) at amino acid position 42 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