17-14301559-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006041.3(HS3ST3B1):āc.41T>Cā(p.Val14Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000189 in 1,588,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006041.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HS3ST3B1 | NM_006041.3 | c.41T>C | p.Val14Ala | missense_variant | 1/2 | ENST00000360954.3 | |
HS3ST3B1 | NR_130138.2 | n.479T>C | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HS3ST3B1 | ENST00000360954.3 | c.41T>C | p.Val14Ala | missense_variant | 1/2 | 1 | NM_006041.3 | P1 | |
HS3ST3B1 | ENST00000466596.5 | c.41T>C | p.Val14Ala | missense_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151410Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000979 AC: 2AN: 204356Hom.: 0 AF XY: 0.00000873 AC XY: 1AN XY: 114510
GnomAD4 exome AF: 6.96e-7 AC: 1AN: 1437190Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 714936
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151410Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73938
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at