rs397516627
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001393500.2(TOMT):āc.573C>Gā(p.Asp191Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,397,674 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D191N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001393500.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TOMT | NM_001393500.2 | c.573C>G | p.Asp191Glu | missense_variant | 3/3 | ENST00000541899.3 | |
LRTOMT | NM_001145309.4 | c.672C>G | p.Asp224Glu | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TOMT | ENST00000541899.3 | c.573C>G | p.Asp191Glu | missense_variant | 3/3 | 5 | NM_001393500.2 | P1 | |
ANAPC15 | ENST00000502597.2 | c.64-1116G>C | intron_variant | 1 | |||||
ANAPC15 | ENST00000543050.5 | c.319-1116G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1397674Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 689398
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 06, 2012 | The Asp224Glu variant in LRTOMT has not been reported in the literature nor prev iously identified by our laboratory. Computational analyses (biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) suggest that the Asp224Glu variant may impact the protein, though this information is not predict ive enough to determine pathogenicity. In summary, additional information is nee ded to fully assess the clinical significance of the Asp224Glu variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at