rs4148945
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004273.5(CHST3):c.*1361C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,750 control chromosomes in the GnomAD database, including 10,783 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.35 ( 10717 hom., cov: 32)
Exomes 𝑓: 0.41 ( 66 hom. )
Consequence
CHST3
NM_004273.5 3_prime_UTR
NM_004273.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.332
Genes affected
CHST3 (HGNC:1971): (carbohydrate sulfotransferase 3) This gene encodes an enzyme which catalyzes the sulfation of chondroitin, a proteoglycan found in the extracellular matrix and most cells which is involved in cell migration and differentiation. Mutations in this gene are associated with spondylepiphyseal dysplasia and humerospinal dysostosis. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 10-72009832-C-T is Benign according to our data. Variant chr10-72009832-C-T is described in ClinVar as [Benign]. Clinvar id is 300606.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST3 | NM_004273.5 | c.*1361C>T | 3_prime_UTR_variant | 3/3 | ENST00000373115.5 | ||
CHST3 | XM_006718075.5 | c.*1361C>T | 3_prime_UTR_variant | 3/3 | |||
CHST3 | XM_011540369.3 | c.*1361C>T | 3_prime_UTR_variant | 3/3 | |||
CHST3 | XM_047426022.1 | c.*1361C>T | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST3 | ENST00000373115.5 | c.*1361C>T | 3_prime_UTR_variant | 3/3 | 1 | NM_004273.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.345 AC: 52475AN: 151924Hom.: 10713 Cov.: 32
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GnomAD4 exome AF: 0.414 AC: 293AN: 708Hom.: 66 Cov.: 0 AF XY: 0.418 AC XY: 213AN XY: 510
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GnomAD4 genome ? AF: 0.345 AC: 52483AN: 152042Hom.: 10717 Cov.: 32 AF XY: 0.341 AC XY: 25320AN XY: 74320
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Skeletal dysplasia Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Spondyloepiphyseal dysplasia congenita Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Larsen syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Spondyloepiphyseal dysplasia with congenital joint dislocations Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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