17-7688404-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018081.2(WRAP53):c.-245G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 558,102 control chromosomes in the GnomAD database, including 278 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_018081.2 5_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 |
---|---|---|---|---|---|---|---|---|
WRAP53 | NM_018081.2 | c.-245G>C | 5_prime_UTR_variant | Exon 1 of 10 | NP_060551.2 | |||
WRAP53 | NM_001143990.2 | c.-1-244G>C | intron_variant | Intron 1 of 10 | NP_001137462.1 | |||
WRAP53 | NM_001143991.2 | c.-1-244G>C | intron_variant | Intron 1 of 10 | NP_001137463.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WRAP53 | ENST00000316024 | c.-245G>C | 5_prime_UTR_variant | Exon 1 of 10 | 1 | ENSP00000324203.5 | ||||
WRAP53 | ENST00000431639.6 | c.-1-244G>C | intron_variant | Intron 1 of 10 | 1 | ENSP00000397219.2 | ||||
WRAP53 | ENST00000457584.6 | c.-1-244G>C | intron_variant | Intron 1 of 10 | 1 | ENSP00000411061.2 |
Frequencies
GnomAD3 genomes AF: 0.0223 AC: 3394AN: 152212Hom.: 57 Cov.: 32
GnomAD4 exome AF: 0.0258 AC: 10489AN: 405772Hom.: 221 Cov.: 3 AF XY: 0.0254 AC XY: 5420AN XY: 213198
GnomAD4 genome AF: 0.0223 AC: 3392AN: 152330Hom.: 57 Cov.: 32 AF XY: 0.0230 AC XY: 1715AN XY: 74488
ClinVar
Submissions by phenotype
Li-Fraumeni syndrome Benign:1
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Dyskeratosis congenita, autosomal recessive 3 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