16-75529432-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_024533.5(CHST5):āc.953C>Gā(p.Thr318Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000049 in 1,612,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T318M) has been classified as Likely benign.
Frequency
Consequence
NM_024533.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHST5 | ENST00000336257.8 | c.953C>G | p.Thr318Arg | missense_variant | Exon 4 of 4 | 1 | NM_024533.5 | ENSP00000338783.3 | ||
ENSG00000260092 | ENST00000460606.1 | n.*1052C>G | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 | ENSP00000457544.1 | ||||
ENSG00000260092 | ENST00000460606.1 | n.*1052C>G | 3_prime_UTR_variant | Exon 5 of 5 | 1 | ENSP00000457544.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000363 AC: 9AN: 248110Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134652
GnomAD4 exome AF: 0.0000466 AC: 68AN: 1460628Hom.: 0 Cov.: 34 AF XY: 0.0000468 AC XY: 34AN XY: 726664
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74454
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at