NM_201631.4:c.1970T>C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_201631.4(TGM5):āc.1970T>Cā(p.Val657Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,614,216 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_201631.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGM5 | NM_201631.4 | c.1970T>C | p.Val657Ala | missense_variant | Exon 12 of 13 | ENST00000220420.10 | NP_963925.2 | |
TGM5 | NM_004245.4 | c.1724T>C | p.Val575Ala | missense_variant | Exon 11 of 12 | NP_004236.1 | ||
TGM5 | XM_011522230.3 | c.941T>C | p.Val314Ala | missense_variant | Exon 6 of 7 | XP_011520532.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGM5 | ENST00000220420.10 | c.1970T>C | p.Val657Ala | missense_variant | Exon 12 of 13 | 1 | NM_201631.4 | ENSP00000220420.5 | ||
TGM5 | ENST00000349114.8 | c.1724T>C | p.Val575Ala | missense_variant | Exon 11 of 12 | 1 | ENSP00000220419.8 | |||
TGM5 | ENST00000396996.3 | n.1446T>C | non_coding_transcript_exon_variant | Exon 5 of 6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00886 AC: 1349AN: 152204Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.00222 AC: 559AN: 251488Hom.: 11 AF XY: 0.00165 AC XY: 224AN XY: 135918
GnomAD4 exome AF: 0.000820 AC: 1199AN: 1461894Hom.: 23 Cov.: 31 AF XY: 0.000708 AC XY: 515AN XY: 727248
GnomAD4 genome AF: 0.00886 AC: 1349AN: 152322Hom.: 16 Cov.: 32 AF XY: 0.00834 AC XY: 621AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
- -
TGM5: BP4, BS1, BS2 -
Acral peeling skin syndrome Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
TGM5-related disorder Benign:1
This variant is classified as 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