rs145607512
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001160372.4(TRAPPC9):c.2796C>T(p.Ala932Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000367 in 1,549,832 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001160372.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000552 AC: 86AN: 155890Hom.: 0 AF XY: 0.000426 AC XY: 35AN XY: 82188
GnomAD4 exome AF: 0.000363 AC: 508AN: 1397538Hom.: 1 Cov.: 34 AF XY: 0.000386 AC XY: 266AN XY: 689432
GnomAD4 genome AF: 0.000401 AC: 61AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:2
TRAPPC9: BP4, BP7 -
- -
Intellectual Disability, Recessive Uncertain:1
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not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
TRAPPC9-related disorder Benign:1
This variant is classified as likely 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