X-132628822-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001394073.1(HS6ST2):āc.1339G>Cā(p.Val447Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,098,043 control chromosomes in the GnomAD database, including 1 homozygotes. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001394073.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HS6ST2 | NM_001394073.1 | c.1339G>C | p.Val447Leu | missense_variant | Exon 5 of 5 | ENST00000370833.7 | NP_001381002.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000552 AC: 10AN: 181321Hom.: 0 AF XY: 0.000104 AC XY: 7AN XY: 67429
GnomAD4 exome AF: 0.0000255 AC: 28AN: 1098043Hom.: 1 Cov.: 32 AF XY: 0.0000440 AC XY: 16AN XY: 363507
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1339G>C (p.V447L) alteration is located in exon 6 (coding exon 5) of the HS6ST2 gene. This alteration results from a G to C substitution at nucleotide position 1339, causing the valine (V) at amino acid position 447 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
HS6ST2: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at