rs535309495
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_004273.5(CHST3):āc.959C>Gā(p.Thr320Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,549,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_004273.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHST3 | NM_004273.5 | c.959C>G | p.Thr320Ser | missense_variant | 3/3 | ENST00000373115.5 | NP_004264.2 | |
CHST3 | XM_006718075.5 | c.959C>G | p.Thr320Ser | missense_variant | 3/3 | XP_006718138.1 | ||
CHST3 | XM_011540369.3 | c.959C>G | p.Thr320Ser | missense_variant | 3/3 | XP_011538671.1 | ||
CHST3 | XM_047426022.1 | c.959C>G | p.Thr320Ser | missense_variant | 3/3 | XP_047281978.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST3 | ENST00000373115.5 | c.959C>G | p.Thr320Ser | missense_variant | 3/3 | 1 | NM_004273.5 | ENSP00000362207.4 |
Frequencies
GnomAD3 genomes AF: 0.000697 AC: 106AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000155 AC: 23AN: 148336Hom.: 0 AF XY: 0.000138 AC XY: 11AN XY: 79494
GnomAD4 exome AF: 0.0000751 AC: 105AN: 1397262Hom.: 0 Cov.: 31 AF XY: 0.0000624 AC XY: 43AN XY: 689172
GnomAD4 genome AF: 0.000696 AC: 106AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.000604 AC XY: 45AN XY: 74470
ClinVar
Submissions by phenotype
Spondyloepiphyseal dysplasia with congenital joint dislocations Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 11, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at