13-96091107-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153456.4(HS6ST3):c.245C>G(p.Pro82Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000353 in 1,417,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153456.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HS6ST3 | NM_153456.4 | c.245C>G | p.Pro82Arg | missense_variant | 1/2 | ENST00000376705.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HS6ST3 | ENST00000376705.4 | c.245C>G | p.Pro82Arg | missense_variant | 1/2 | 1 | NM_153456.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000133 AC: 2AN: 149926Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000233 AC: 1AN: 42990Hom.: 0 AF XY: 0.0000446 AC XY: 1AN XY: 22436
GnomAD4 exome AF: 0.00000237 AC: 3AN: 1267194Hom.: 0 Cov.: 32 AF XY: 0.00000324 AC XY: 2AN XY: 616348
GnomAD4 genome ? AF: 0.0000133 AC: 2AN: 149926Hom.: 0 Cov.: 30 AF XY: 0.0000137 AC XY: 1AN XY: 73160
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.245C>G (p.P82R) alteration is located in exon 1 (coding exon 1) of the HS6ST3 gene. This alteration results from a C to G substitution at nucleotide position 245, causing the proline (P) at amino acid position 82 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at