chr19-45163979-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001270891.2(TRAPPC6A):c.385G>A(p.Gly129Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000234 in 1,578,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001270891.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000523 AC: 1AN: 191138Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 101810
GnomAD4 exome AF: 0.0000217 AC: 31AN: 1426764Hom.: 0 Cov.: 33 AF XY: 0.0000212 AC XY: 15AN XY: 706062
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.427G>A (p.G143S) alteration is located in exon 5 (coding exon 5) of the TRAPPC6A gene. This alteration results from a G to A substitution at nucleotide position 427, causing the glycine (G) at amino acid position 143 to be replaced by a serine (S). 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