1-58576137-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002353.3(TACSTD2):c.*48G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 1,596,804 control chromosomes in the GnomAD database, including 6,675 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002353.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0774 AC: 11779AN: 152176Hom.: 488 Cov.: 33
GnomAD3 exomes AF: 0.0761 AC: 17051AN: 224032Hom.: 732 AF XY: 0.0785 AC XY: 9472AN XY: 120604
GnomAD4 exome AF: 0.0890 AC: 128589AN: 1444510Hom.: 6186 Cov.: 30 AF XY: 0.0893 AC XY: 64056AN XY: 717338
GnomAD4 genome AF: 0.0774 AC: 11788AN: 152294Hom.: 489 Cov.: 33 AF XY: 0.0752 AC XY: 5601AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
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Gelatinous droplike corneal dystrophy 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at