rs764380548
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_000359.3(TGM1):c.2066G>A(p.Arg689His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R689R) has been classified as Likely benign.
Frequency
Consequence
NM_000359.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGM1 | NM_000359.3 | c.2066G>A | p.Arg689His | missense_variant | 13/15 | ENST00000206765.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGM1 | ENST00000206765.11 | c.2066G>A | p.Arg689His | missense_variant | 13/15 | 1 | NM_000359.3 | P1 | |
TGM1 | ENST00000544573.5 | c.740G>A | p.Arg247His | missense_variant | 7/9 | 2 | |||
TGM1 | ENST00000559669.1 | c.224G>A | p.Arg75His | missense_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251132Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135796
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461584Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 727088
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74382
ClinVar
Submissions by phenotype
Autosomal recessive congenital ichthyosis 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Oct 03, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at