X-132628495-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001394073.1(HS6ST2):c.1666G>A(p.Glu556Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 1,097,969 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001394073.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HS6ST2 | NM_001394073.1 | c.1666G>A | p.Glu556Lys | missense_variant | Exon 5 of 5 | ENST00000370833.7 | NP_001381002.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097969Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363451
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
HS6ST2-related disorder Uncertain:1
The HS6ST2 c.1666G>A variant is predicted to result in the amino acid substitution p.Glu556Lys. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at