rs835487
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018413.6(CHST11):c.204+64998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,052 control chromosomes in the GnomAD database, including 15,045 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.43 ( 15045 hom., cov: 32)
Consequence
CHST11
NM_018413.6 intron
NM_018413.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.966
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST11 | NM_018413.6 | c.204+64998A>G | intron_variant | ENST00000303694.6 | |||
CHST11 | NM_001173982.2 | c.189+64998A>G | intron_variant | ||||
CHST11 | XM_047428914.1 | c.-33-89960A>G | intron_variant | ||||
CHST11 | XM_047428915.1 | c.-33-89960A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST11 | ENST00000303694.6 | c.204+64998A>G | intron_variant | 1 | NM_018413.6 | P4 | |||
CHST11 | ENST00000549260.5 | c.189+64998A>G | intron_variant | 1 | A1 | ||||
CHST11 | ENST00000549016.1 | c.84+64998A>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.428 AC: 64962AN: 151934Hom.: 14998 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.428 AC: 65064AN: 152052Hom.: 15045 Cov.: 32 AF XY: 0.424 AC XY: 31544AN XY: 74312
GnomAD4 genome
?
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32
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31544
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1596
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at