ENST00000683983.1:c.12G>A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PVS1_StrongBS1_SupportingBS2
The ENST00000683983.1(TRAPPC2):c.12G>A(p.Trp4*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000452 in 511,094 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 83 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000683983.1 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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TRAPPC2 | ENST00000683983.1 | c.12G>A | p.Trp4* | stop_gained | Exon 2 of 6 | ENSP00000507474.1 | ||||
TRAPPC2 | ENST00000380579.6 | c.-97G>A | 5_prime_UTR_variant | Exon 2 of 6 | 1 | NM_001011658.4 | ENSP00000369953.1 | |||
TRAPPC2 | ENST00000359680.9 | c.-20+404G>A | intron_variant | Intron 1 of 4 | 1 | ENSP00000352708.5 | ||||
TRAPPC2 | ENST00000458511.7 | c.-90+404G>A | intron_variant | Intron 1 of 5 | 5 | ENSP00000392495.3 | ||||
TRAPPC2 | ENST00000519885.5 | c.-20+404G>A | intron_variant | Intron 1 of 3 | 3 | ENSP00000430725.1 |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 36AN: 111900Hom.: 0 Cov.: 23 AF XY: 0.000293 AC XY: 10AN XY: 34084
GnomAD3 exomes AF: 0.000394 AC: 37AN: 93930Hom.: 0 AF XY: 0.000336 AC XY: 11AN XY: 32784
GnomAD4 exome AF: 0.000488 AC: 195AN: 399194Hom.: 0 Cov.: 0 AF XY: 0.000497 AC XY: 73AN XY: 146744
GnomAD4 genome AF: 0.000322 AC: 36AN: 111900Hom.: 0 Cov.: 23 AF XY: 0.000293 AC XY: 10AN XY: 34084
ClinVar
Submissions by phenotype
Spondyloepiphyseal dysplasia tarda Pathogenic:2Benign:1
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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 specified Uncertain:1
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not provided Benign:1
TRAPPC2: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at