rs10865541
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4BS1
The NM_016030.6(TRAPPC12):c.681T>A(p.Phe227Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000934 in 1,606,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F227S) 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.681T>A | p.Phe227Leu | missense_variant | 2/12 | ENST00000324266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC12 | ENST00000324266.10 | c.681T>A | p.Phe227Leu | missense_variant | 2/12 | 1 | NM_016030.6 | P1 | |
TRAPPC12 | ENST00000382110.6 | c.681T>A | p.Phe227Leu | missense_variant | 2/12 | 2 | P1 | ||
TRAPPC12 | ENST00000482645.1 | n.842T>A | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
TRAPPC12 | ENST00000411973.3 | c.180T>A | p.Phe60Leu | missense_variant, NMD_transcript_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151852Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000297 AC: 7AN: 235766Hom.: 0 AF XY: 0.0000312 AC XY: 4AN XY: 128406
GnomAD4 exome AF: 0.00000756 AC: 11AN: 1454836Hom.: 0 Cov.: 62 AF XY: 0.00000829 AC XY: 6AN XY: 723756
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151960Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74276
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at