19-45164934-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001270892.2(TRAPPC6A):c.163G>A(p.Gly55Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000665 in 1,614,160 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001270892.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00363 AC: 552AN: 152222Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00101 AC: 254AN: 251392Hom.: 1 AF XY: 0.000795 AC XY: 108AN XY: 135886
GnomAD4 exome AF: 0.000356 AC: 521AN: 1461820Hom.: 4 Cov.: 31 AF XY: 0.000297 AC XY: 216AN XY: 727224
GnomAD4 genome AF: 0.00362 AC: 552AN: 152340Hom.: 5 Cov.: 33 AF XY: 0.00341 AC XY: 254AN XY: 74488
ClinVar
Submissions by phenotype
TRAPPC6A-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at