12-104756989-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018413.6(CHST11):c.245G>A(p.Arg82Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,459,860 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
Genome browser will be placed here
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.245G>A | p.Arg82Gln | missense_variant | Exon 3 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.230G>A | p.Arg77Gln | missense_variant | Exon 3 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.8G>A | p.Arg3Gln | missense_variant | Exon 2 of 2 | XP_047284870.1 | ||
CHST11 | XM_047428915.1 | c.8G>A | p.Arg3Gln | 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.245G>A | p.Arg82Gln | missense_variant | Exon 3 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
CHST11 | ENST00000549260.5 | c.230G>A | p.Arg77Gln | missense_variant | Exon 3 of 3 | 1 | ENSP00000450004.1 | |||
CHST11 | ENST00000549016.1 | c.125G>A | p.Arg42Gln | missense_variant | Exon 3 of 3 | 4 | ENSP00000449095.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247742Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134490
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1459860Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726358
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.245G>A (p.R82Q) alteration is located in exon 3 (coding exon 3) of the CHST11 gene. This alteration results from a G to A substitution at nucleotide position 245, causing the arginine (R) at amino acid position 82 to be replaced by a glutamine (Q). 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