15-43234871-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBS2_Supporting
The NM_201631.4(TGM5):c.1773C>T(p.Asp591Asp) variant causes a synonymous change. The variant allele was found at a frequency of 0.00318 in 1,614,242 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_201631.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGM5 | NM_201631.4 | c.1773C>T | p.Asp591Asp | synonymous_variant | Exon 11 of 13 | ENST00000220420.10 | NP_963925.2 | |
TGM5 | NM_004245.4 | c.1527C>T | p.Asp509Asp | synonymous_variant | Exon 10 of 12 | NP_004236.1 | ||
TGM5 | XM_011522230.3 | c.744C>T | p.Asp248Asp | synonymous_variant | Exon 5 of 7 | XP_011520532.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGM5 | ENST00000220420.10 | c.1773C>T | p.Asp591Asp | synonymous_variant | Exon 11 of 13 | 1 | NM_201631.4 | ENSP00000220420.5 | ||
TGM5 | ENST00000349114.8 | c.1527C>T | p.Asp509Asp | synonymous_variant | Exon 10 of 12 | 1 | ENSP00000220419.8 | |||
TGM5 | ENST00000396996.3 | n.1249C>T | non_coding_transcript_exon_variant | Exon 4 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00227 AC: 346AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00234 AC: 589AN: 251486Hom.: 3 AF XY: 0.00238 AC XY: 324AN XY: 135916
GnomAD4 exome AF: 0.00328 AC: 4791AN: 1461876Hom.: 9 Cov.: 32 AF XY: 0.00321 AC XY: 2332AN XY: 727238
GnomAD4 genome AF: 0.00227 AC: 346AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.00227 AC XY: 169AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:3
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TGM5: BP4, BS2 -
- -
Acral peeling skin syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
TGM5-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at