rs9903215
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001159773.2(CANT1):c.967G>T(p.Ala323Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign 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. A323T) has been classified as Likely benign.
Frequency
Consequence
NM_001159773.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CANT1 | NM_001159773.2 | c.967G>T | p.Ala323Ser | missense_variant | 5/5 | ENST00000392446.10 | |
CANT1 | NM_001159772.2 | c.967G>T | p.Ala323Ser | missense_variant | 6/6 | ||
CANT1 | NM_138793.4 | c.967G>T | p.Ala323Ser | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CANT1 | ENST00000392446.10 | c.967G>T | p.Ala323Ser | missense_variant | 5/5 | 1 | NM_001159773.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248812Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134828
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459432Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 725992
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at