19-45164900-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001270891.2(TRAPPC6A):c.223G>A(p.Val75Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000273 in 1,614,148 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001270891.2 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: 0.000302 AC: 46AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000692 AC: 174AN: 251392Hom.: 0 AF XY: 0.000618 AC XY: 84AN XY: 135898
GnomAD4 exome AF: 0.000270 AC: 395AN: 1461808Hom.: 2 Cov.: 31 AF XY: 0.000272 AC XY: 198AN XY: 727218
GnomAD4 genome AF: 0.000302 AC: 46AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74490
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