X-132628506-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001394073.1(HS6ST2):c.1655G>A(p.Arg552Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000662 in 1,208,986 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394073.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HS6ST2 | NM_001394073.1 | c.1655G>A | p.Arg552Gln | missense_variant | Exon 5 of 5 | ENST00000370833.7 | NP_001381002.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000180 AC: 2AN: 111023Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33213
GnomAD4 exome AF: 0.00000546 AC: 6AN: 1097963Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 3AN XY: 363433
GnomAD4 genome AF: 0.0000180 AC: 2AN: 111023Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33213
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1655G>A (p.R552Q) alteration is located in exon 6 (coding exon 5) of the HS6ST2 gene. This alteration results from a G to A substitution at nucleotide position 1655, causing the arginine (R) at amino acid position 552 to be replaced by a glutamine (Q). 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