12-104757414-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018413.6(CHST11):āc.670G>Cā(p.Ala224Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00371 in 1,613,938 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_018413.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.670G>C | p.Ala224Pro | missense_variant | Exon 3 of 3 | ENST00000303694.6 | NP_060883.1 | |
CHST11 | NM_001173982.2 | c.655G>C | p.Ala219Pro | missense_variant | Exon 3 of 3 | NP_001167453.1 | ||
CHST11 | XM_047428914.1 | c.433G>C | p.Ala145Pro | missense_variant | Exon 2 of 2 | XP_047284870.1 | ||
CHST11 | XM_047428915.1 | c.433G>C | p.Ala145Pro | 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.670G>C | p.Ala224Pro | missense_variant | Exon 3 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
CHST11 | ENST00000549260.5 | c.655G>C | p.Ala219Pro | missense_variant | Exon 3 of 3 | 1 | ENSP00000450004.1 |
Frequencies
GnomAD3 genomes AF: 0.00271 AC: 411AN: 151928Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00261 AC: 656AN: 251464Hom.: 1 AF XY: 0.00255 AC XY: 347AN XY: 135916
GnomAD4 exome AF: 0.00381 AC: 5571AN: 1461892Hom.: 17 Cov.: 31 AF XY: 0.00366 AC XY: 2659AN XY: 727246
GnomAD4 genome AF: 0.00270 AC: 411AN: 152046Hom.: 2 Cov.: 32 AF XY: 0.00256 AC XY: 190AN XY: 74300
ClinVar
Submissions by phenotype
not provided Benign:1
CHST11: BS2 -
CHST11-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at