X-132628513-C-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001394073.1(HS6ST2):c.1648G>T(p.Ala550Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00215 in 1,209,099 control chromosomes in the GnomAD database, including 5 homozygotes. There are 815 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001394073.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HS6ST2 | NM_001394073.1 | c.1648G>T | p.Ala550Ser | missense_variant | Exon 5 of 5 | ENST00000370833.7 | NP_001381002.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00141 AC: 157AN: 111057Hom.: 0 Cov.: 22 AF XY: 0.00138 AC XY: 46AN XY: 33245
GnomAD3 exomes AF: 0.00151 AC: 273AN: 180719Hom.: 0 AF XY: 0.00152 AC XY: 102AN XY: 67063
GnomAD4 exome AF: 0.00223 AC: 2444AN: 1097991Hom.: 5 Cov.: 31 AF XY: 0.00212 AC XY: 769AN XY: 363459
GnomAD4 genome AF: 0.00141 AC: 157AN: 111108Hom.: 0 Cov.: 22 AF XY: 0.00138 AC XY: 46AN XY: 33306
ClinVar
Submissions by phenotype
HS6ST2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at