2-3387867-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016030.6(TRAPPC12):c.244G>A(p.Ala82Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000232 in 1,594,170 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 (★).
Frequency
Consequence
NM_016030.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC12 | NM_016030.6 | c.244G>A | p.Ala82Thr | missense_variant | 2/12 | ENST00000324266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC12 | ENST00000324266.10 | c.244G>A | p.Ala82Thr | missense_variant | 2/12 | 1 | NM_016030.6 | P1 | |
TRAPPC12 | ENST00000382110.6 | c.244G>A | p.Ala82Thr | missense_variant | 2/12 | 2 | P1 | ||
TRAPPC12 | ENST00000482645.1 | n.405G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000345 AC: 8AN: 232088Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126114
GnomAD4 exome AF: 0.0000229 AC: 33AN: 1441876Hom.: 0 Cov.: 31 AF XY: 0.0000168 AC XY: 12AN XY: 714290
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74470
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2021 | The c.244G>A (p.A82T) alteration is located in exon 2 (coding exon 1) of the TRAPPC12 gene. This alteration results from a G to A substitution at nucleotide position 244, causing the alanine (A) at amino acid position 82 to be replaced by a threonine (T). 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