21-44055771-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003274.5(TRAPPC10):c.556C>A(p.Leu186Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003274.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAPPC10 | ENST00000291574.9 | c.556C>A | p.Leu186Ile | missense_variant | Exon 5 of 23 | 1 | NM_003274.5 | ENSP00000291574.4 | ||
TRAPPC10 | ENST00000380221.7 | c.556C>A | p.Leu186Ile | missense_variant | Exon 5 of 7 | 1 | ENSP00000369570.3 | |||
TRAPPC10 | ENST00000422875.5 | n.556C>A | non_coding_transcript_exon_variant | Exon 5 of 24 | 1 | ENSP00000402221.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461676Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727118
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.556C>A (p.L186I) alteration is located in exon 5 (coding exon 5) of the TRAPPC10 gene. This alteration results from a C to A substitution at nucleotide position 556, causing the leucine (L) at amino acid position 186 to be replaced by an isoleucine (I). 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