2-3387697-A-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_016030.6(TRAPPC12):c.74A>T(p.Glu25Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,580,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E25L) has been classified as Uncertain significance.
Frequency
Consequence
NM_016030.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC12 | NM_016030.6 | c.74A>T | p.Glu25Val | missense_variant | 2/12 | ENST00000324266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC12 | ENST00000324266.10 | c.74A>T | p.Glu25Val | missense_variant | 2/12 | 1 | NM_016030.6 | P1 | |
TRAPPC12 | ENST00000382110.6 | c.74A>T | p.Glu25Val | missense_variant | 2/12 | 2 | P1 | ||
TRAPPC12 | ENST00000482645.1 | n.235A>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152114Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000253 AC: 5AN: 197934Hom.: 0 AF XY: 0.0000188 AC XY: 2AN XY: 106664
GnomAD4 exome AF: 0.0000126 AC: 18AN: 1428764Hom.: 0 Cov.: 31 AF XY: 0.0000155 AC XY: 11AN XY: 707932
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15AN XY: 74314
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.74A>T (p.E25V) alteration is located in exon 2 (coding exon 1) of the TRAPPC12 gene. This alteration results from a A to T substitution at nucleotide position 74, causing the glutamic acid (E) at amino acid position 25 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at