20-2403432-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 3P and 13B. PM5PP3BP4BP6_Very_StrongBS2
The NM_198994.3(TGM6):c.1025G>A(p.Arg342Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,614,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R342W) has been classified as Likely pathogenic.
Frequency
Consequence
NM_198994.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGM6 | NM_198994.3 | c.1025G>A | p.Arg342Gln | missense_variant | 8/13 | ENST00000202625.7 | |
TGM6 | NM_001254734.2 | c.1025G>A | p.Arg342Gln | missense_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGM6 | ENST00000202625.7 | c.1025G>A | p.Arg342Gln | missense_variant | 8/13 | 1 | NM_198994.3 | P1 | |
TGM6 | ENST00000381423.1 | c.1025G>A | p.Arg342Gln | missense_variant | 8/12 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000658 AC: 100AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251454Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135908
GnomAD4 exome AF: 0.0000862 AC: 126AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000784 AC XY: 57AN XY: 727242
GnomAD4 genome AF: 0.000650 AC: 99AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 27, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 18, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at