7-2432644-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018641.5(CHST12):c.5C>T(p.Thr2Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,605,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018641.5 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 |
---|---|---|---|---|---|---|---|
CHST12 | NM_018641.5 | c.5C>T | p.Thr2Ile | missense_variant | 2/2 | ENST00000618655.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST12 | ENST00000618655.2 | c.5C>T | p.Thr2Ile | missense_variant | 2/2 | 1 | NM_018641.5 | P1 | |
CHST12 | ENST00000258711.7 | c.5C>T | p.Thr2Ile | missense_variant | 2/2 | 1 | P1 | ||
CHST12 | ENST00000432336.1 | c.5C>T | p.Thr2Ile | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000363 AC: 9AN: 247770Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134170
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1453346Hom.: 0 Cov.: 31 AF XY: 0.0000125 AC XY: 9AN XY: 721210
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at