chr13-96091562-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_153456.4(HS6ST3):c.700C>T(p.His234Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000178 in 1,575,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153456.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HS6ST3 | NM_153456.4 | c.700C>T | p.His234Tyr | missense_variant | 1/2 | ENST00000376705.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HS6ST3 | ENST00000376705.4 | c.700C>T | p.His234Tyr | missense_variant | 1/2 | 1 | NM_153456.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152092Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000367 AC: 7AN: 190550Hom.: 0 AF XY: 0.0000575 AC XY: 6AN XY: 104294
GnomAD4 exome AF: 0.0000176 AC: 25AN: 1423596Hom.: 0 Cov.: 33 AF XY: 0.0000312 AC XY: 22AN XY: 706148
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152208Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2023 | The c.700C>T (p.H234Y) alteration is located in exon 1 (coding exon 1) of the HS6ST3 gene. This alteration results from a C to T substitution at nucleotide position 700, causing the histidine (H) at amino acid position 234 to be replaced by a tyrosine (Y). 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