chr10-71964529-GC-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_004273.5(CHST3):c.-270del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 152,142 control chromosomes in the GnomAD database, including 45 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.014 ( 45 hom., cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CHST3
NM_004273.5 5_prime_UTR
NM_004273.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.19
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 -10 ACMG points.
BP6
?
Variant 10-71964529-GC-G is Benign according to our data. Variant chr10-71964529-GC-G is described in ClinVar as [Likely_benign]. Clinvar id is 300550.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0141 (2141/152142) while in subpopulation AFR AF= 0.0469 (1950/41542). AF 95% confidence interval is 0.0452. There are 45 homozygotes in gnomad4. There are 1007 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 44 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST3 | NM_004273.5 | c.-270del | 5_prime_UTR_variant | 1/3 | ENST00000373115.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST3 | ENST00000373115.5 | c.-270del | 5_prime_UTR_variant | 1/3 | 1 | NM_004273.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0141 AC: 2140AN: 152034Hom.: 44 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 38Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 22
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GnomAD4 genome ? AF: 0.0141 AC: 2141AN: 152142Hom.: 45 Cov.: 33 AF XY: 0.0135 AC XY: 1007AN XY: 74392
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Skeletal dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Spondyloepiphyseal dysplasia congenita Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Larsen syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Spondyloepiphyseal dysplasia with congenital joint dislocations Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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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