rs121918730
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The ENST00000206765.11(TGM1):āc.866A>Gā(p.Asn289Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,768 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. N289T) has been classified as Pathogenic.
Frequency
Consequence
ENST00000206765.11 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGM1 | NM_000359.3 | c.866A>G | p.Asn289Ser | missense_variant | 5/15 | ENST00000206765.11 | NP_000350.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGM1 | ENST00000206765.11 | c.866A>G | p.Asn289Ser | missense_variant | 5/15 | 1 | NM_000359.3 | ENSP00000206765 | P1 | |
TGM1 | ENST00000559136.1 | c.-62A>G | 5_prime_UTR_variant | 1/7 | 5 | ENSP00000453337 | ||||
TGM1 | ENST00000544573.5 | c.-28-1562A>G | intron_variant | 2 | ENSP00000439446 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251398Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135906
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461768Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727198
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at