NM_001394073.1:c.1226A>G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001394073.1(HS6ST2):āc.1226A>Gā(p.Asp409Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,209,505 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001394073.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HS6ST2 | NM_001394073.1 | c.1226A>G | p.Asp409Gly | missense_variant | Exon 5 of 5 | ENST00000370833.7 | NP_001381002.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 12AN: 111672Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33826
GnomAD3 exomes AF: 0.0000333 AC: 6AN: 180387Hom.: 0 AF XY: 0.0000450 AC XY: 3AN XY: 66683
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1097833Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 363343
GnomAD4 genome AF: 0.000107 AC: 12AN: 111672Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33826
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1226A>G (p.D409G) alteration is located in exon 6 (coding exon 5) of the HS6ST2 gene. This alteration results from a A to G substitution at nucleotide position 1226, causing the aspartic acid (D) at amino acid position 409 to be replaced by a glycine (G). 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