15-43232939-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_201631.4(TGM5):c.*252C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 514,540 control chromosomes in the GnomAD database, including 679 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_201631.4 3_prime_UTR
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.*252C>T | 3_prime_UTR_variant | Exon 13 of 13 | ENST00000220420.10 | NP_963925.2 | ||
TGM5 | NM_004245.4 | c.*252C>T | 3_prime_UTR_variant | Exon 12 of 12 | NP_004236.1 | |||
TGM5 | XM_011522230.3 | c.*252C>T | 3_prime_UTR_variant | Exon 7 of 7 | XP_011520532.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0449 AC: 6825AN: 152148Hom.: 511 Cov.: 32
GnomAD4 exome AF: 0.00802 AC: 2904AN: 362274Hom.: 159 Cov.: 3 AF XY: 0.00723 AC XY: 1388AN XY: 191924
GnomAD4 genome AF: 0.0451 AC: 6863AN: 152266Hom.: 520 Cov.: 32 AF XY: 0.0424 AC XY: 3154AN XY: 74464
ClinVar
Submissions by phenotype
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at