12-104757034-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018413.6(CHST11):c.290G>A(p.Arg97His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.290G>A | p.Arg97His | missense_variant | Exon 3 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.275G>A | p.Arg92His | missense_variant | Exon 3 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.53G>A | p.Arg18His | missense_variant | Exon 2 of 2 | XP_047284870.1 | ||
CHST11 | XM_047428915.1 | c.53G>A | p.Arg18His | 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.290G>A | p.Arg97His | missense_variant | Exon 3 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
CHST11 | ENST00000549260.5 | c.275G>A | p.Arg92His | missense_variant | Exon 3 of 3 | 1 | ENSP00000450004.1 | |||
CHST11 | ENST00000549016.1 | c.170G>A | p.Arg57His | missense_variant | Exon 3 of 3 | 4 | ENSP00000449095.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000997 AC: 25AN: 250642Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135730
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727206
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.290G>A (p.R97H) 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 290, causing the arginine (R) at amino acid position 97 to be replaced by a histidine (H). 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