rs372896864
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_201631.4(TGM5):āc.2010C>Gā(p.Phe670Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 18/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_201631.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGM5 | NM_201631.4 | c.2010C>G | p.Phe670Leu | missense_variant, splice_region_variant | Exon 13 of 13 | ENST00000220420.10 | NP_963925.2 | |
TGM5 | NM_004245.4 | c.1764C>G | p.Phe588Leu | missense_variant, splice_region_variant | Exon 12 of 12 | NP_004236.1 | ||
TGM5 | XM_011522230.3 | c.981C>G | p.Phe327Leu | missense_variant, splice_region_variant | Exon 7 of 7 | XP_011520532.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGM5 | ENST00000220420.10 | c.2010C>G | p.Phe670Leu | missense_variant, splice_region_variant | Exon 13 of 13 | 1 | NM_201631.4 | ENSP00000220420.5 | ||
TGM5 | ENST00000349114.8 | c.1764C>G | p.Phe588Leu | missense_variant, splice_region_variant | Exon 12 of 12 | 1 | ENSP00000220419.8 | |||
TGM5 | ENST00000396996.3 | n.1486C>G | splice_region_variant, non_coding_transcript_exon_variant | Exon 6 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461338Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726998
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74288
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at