rs58718148
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_006042.3(HS3ST3A1):c.-798delC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.99 ( 74673 hom., cov: 0)
Exomes 𝑓: 1.0 ( 286 hom. )
Consequence
HS3ST3A1
NM_006042.3 5_prime_UTR
NM_006042.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.187
Genes affected
HS3ST3A1 (HGNC:5196): (heparan sulfate-glucosamine 3-sulfotransferase 3A1) Heparan sulfate biosynthetic enzymes are key components in generating a myriad of distinct heparan sulfate fine structures that carry out multiple biologic activities. The enzyme encoded by this gene is a member of the heparan sulfate biosynthetic enzyme family. It is a type II integral membrane protein and possesses heparan sulfate glucosaminyl 3-O-sulfotransferase activity. The sulfotransferase domain of this enzyme is highly similar to the same domain of heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3B1, and these two enzymes sulfate an identical disaccharide. This gene is widely expressed, with the most abundant expression in liver and placenta. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HS3ST3A1 | NM_006042.3 | c.-798delC | 5_prime_UTR_variant | 1/2 | ENST00000284110.2 | NP_006033.1 | ||
HS3ST3A1 | XM_017025480.3 | c.-798delC | 5_prime_UTR_variant | 1/2 | XP_016880969.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HS3ST3A1 | ENST00000284110.2 | c.-798delC | 5_prime_UTR_variant | 1/2 | 1 | NM_006042.3 | ENSP00000284110.1 |
Frequencies
GnomAD3 genomes AF: 0.990 AC: 150686AN: 152170Hom.: 74617 Cov.: 0
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GnomAD4 exome AF: 0.998 AC: 573AN: 574Hom.: 286 Cov.: 0 AF XY: 1.00 AC XY: 414AN XY: 414
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GnomAD4 genome AF: 0.990 AC: 150796AN: 152278Hom.: 74673 Cov.: 0 AF XY: 0.991 AC XY: 73751AN XY: 74458
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at