17-14301846-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006041.3(HS3ST3B1):c.328A>T(p.Ser110Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000597 in 1,591,254 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_006041.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HS3ST3B1 | NM_006041.3 | c.328A>T | p.Ser110Cys | missense_variant | 1/2 | ENST00000360954.3 | |
HS3ST3B1 | NR_130138.2 | n.766A>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HS3ST3B1 | ENST00000360954.3 | c.328A>T | p.Ser110Cys | missense_variant | 1/2 | 1 | NM_006041.3 | P1 | |
HS3ST3B1 | ENST00000466596.5 | c.328A>T | p.Ser110Cys | missense_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000870 AC: 18AN: 206822Hom.: 0 AF XY: 0.0000888 AC XY: 10AN XY: 112660
GnomAD4 exome AF: 0.0000257 AC: 37AN: 1438980Hom.: 0 Cov.: 31 AF XY: 0.0000280 AC XY: 20AN XY: 713396
GnomAD4 genome AF: 0.000381 AC: 58AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.328A>T (p.S110C) alteration is located in exon 1 (coding exon 1) of the HS3ST3B1 gene. This alteration results from a A to T substitution at nucleotide position 328, causing the serine (S) at amino acid position 110 to be replaced by a cysteine (C). 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