rs148230565
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018413.6(CHST11):c.670G>A(p.Ala224Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
CHST11
NM_018413.6 missense
NM_018413.6 missense
Scores
2
10
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.69
Genes affected
CHST11 (HGNC:17422): (carbohydrate sulfotransferase 11) The protein encoded by this gene belongs to the sulfotransferase 2 family. It is localized to the golgi membrane, and catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage, and is distributed on the surfaces of many cells and extracellular matrices. A chromosomal translocation involving this gene and IgH, t(12;14)(q23;q32), has been reported in a patient with B-cell chronic lymphocytic leukemia. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CHST11 | NM_018413.6 | c.670G>A | p.Ala224Thr | missense_variant | Exon 3 of 3 | ENST00000303694.6 | NP_060883.1 | |
| CHST11 | NM_001173982.2 | c.655G>A | p.Ala219Thr | missense_variant | Exon 3 of 3 | NP_001167453.1 | ||
| CHST11 | XM_047428914.1 | c.433G>A | p.Ala145Thr | missense_variant | Exon 2 of 2 | XP_047284870.1 | ||
| CHST11 | XM_047428915.1 | c.433G>A | p.Ala145Thr | 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>A | p.Ala224Thr | missense_variant | Exon 3 of 3 | 1 | NM_018413.6 | ENSP00000305725.5 | ||
| CHST11 | ENST00000549260.5 | c.655G>A | p.Ala219Thr | missense_variant | Exon 3 of 3 | 1 | ENSP00000450004.1 | |||
| CHST11 | ENST00000549016.1 | c.*75G>A | downstream_gene_variant | 4 | ENSP00000449095.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727246
GnomAD4 exome
AF:
AC:
4
AN:
1461892
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
727246
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T
MetaSVM
Uncertain
T
MutationAssessor
Benign
.;L
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Benign
T;D
Polyphen
D;D
Vest4
MutPred
0.55
.;Gain of phosphorylation at A224 (P = 0.0571);
MVP
MPC
1.7
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at