rs483981
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013352.4(DSE):c.*4569T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,152 control chromosomes in the GnomAD database, including 51,849 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 0.82 ( 51840 hom., cov: 31)
Exomes 𝑓: 0.82 ( 9 hom. )
Consequence
DSE
NM_013352.4 3_prime_UTR
NM_013352.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.22
Genes affected
DSE (HGNC:21144): (dermatan sulfate epimerase) The protein encoded by this gene is a tumor-rejection antigen. It is localized to the endoplasmic reticulum and functions to convert D-glucuronic acid to L-iduronic acid during the biosynthesis of dermatan sulfate. This antigen possesses tumor epitopes capable of inducing HLA-A24-restricted and tumor-specific cytotoxic T lymphocytes in cancer patients and may be useful for specific immunotherapy. Mutations in this gene cause inmusculocontractural Ehlers-Danlos syndrome. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 9, and a paralogous gene exists on chromosome 18. [provided by RefSeq, Apr 2016]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSE | NM_013352.4 | c.*4569T>C | 3_prime_UTR_variant | 6/6 | ENST00000644252.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSE | ENST00000644252.3 | c.*4569T>C | 3_prime_UTR_variant | 6/6 | NM_013352.4 | P1 | |||
DSE | ENST00000452085.7 | c.*4569T>C | 3_prime_UTR_variant | 6/6 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.818 AC: 124411AN: 152006Hom.: 51786 Cov.: 31
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GnomAD4 exome AF: 0.821 AC: 23AN: 28Hom.: 9 Cov.: 0 AF XY: 0.714 AC XY: 10AN XY: 14
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GnomAD4 genome ? AF: 0.819 AC: 124524AN: 152124Hom.: 51840 Cov.: 31 AF XY: 0.816 AC XY: 60646AN XY: 74350
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ClinVar
Not reported inComputational scores
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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