chr7-100157720-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018275.5(TRAPPC14):c.550G>A(p.Val184Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00471 in 1,614,222 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018275.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00311 AC: 473AN: 152222Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00359 AC: 903AN: 251452Hom.: 4 AF XY: 0.00396 AC XY: 538AN XY: 135902
GnomAD4 exome AF: 0.00488 AC: 7137AN: 1461882Hom.: 31 Cov.: 32 AF XY: 0.00508 AC XY: 3694AN XY: 727240
GnomAD4 genome AF: 0.00310 AC: 473AN: 152340Hom.: 1 Cov.: 33 AF XY: 0.00289 AC XY: 215AN XY: 74502
ClinVar
Submissions by phenotype
TRAPPC14-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 25, 2019 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | TRAPPC14: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at