rs10227362
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018641.5(CHST12):c.-78+13491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 151,934 control chromosomes in the GnomAD database, including 54,206 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 0.84 ( 54206 hom., cov: 29)
Consequence
CHST12
NM_018641.5 intron
NM_018641.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.950
Genes affected
CHST12 (HGNC:17423): (carbohydrate sulfotransferase 12) 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 and desulfated dermatan sulfate. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage, and is distributed on the surfaces of many cells and extracellular matrices. Alternatively spliced transcript variants differing only in their 5' UTRs 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=-1.01).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST12 | NM_018641.5 | c.-78+13491A>G | intron_variant | ENST00000618655.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST12 | ENST00000618655.2 | c.-78+13491A>G | intron_variant | 1 | NM_018641.5 | P1 | |||
CHST12 | ENST00000258711.7 | c.-78+13519A>G | intron_variant | 1 | P1 | ||||
CHST12 | ENST00000432336.1 | c.-78+12958A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.842 AC: 127829AN: 151816Hom.: 54155 Cov.: 29
GnomAD3 genomes
?
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.842 AC: 127936AN: 151934Hom.: 54206 Cov.: 29 AF XY: 0.839 AC XY: 62280AN XY: 74230
GnomAD4 genome
?
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151934
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29
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62280
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74230
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2930
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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