10-72008083-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_004273.5(CHST3):c.1052C>T(p.Ser351Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000718 in 1,393,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S351Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_004273.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST3 | NM_004273.5 | c.1052C>T | p.Ser351Phe | missense_variant | 3/3 | ENST00000373115.5 | |
CHST3 | XM_006718075.5 | c.1052C>T | p.Ser351Phe | missense_variant | 3/3 | ||
CHST3 | XM_011540369.3 | c.1052C>T | p.Ser351Phe | missense_variant | 3/3 | ||
CHST3 | XM_047426022.1 | c.1052C>T | p.Ser351Phe | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST3 | ENST00000373115.5 | c.1052C>T | p.Ser351Phe | missense_variant | 3/3 | 1 | NM_004273.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.18e-7 AC: 1AN: 1393272Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 686952
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at