chr19-45163182-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001270891.2(TRAPPC6A):c.*10G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 1,613,814 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001270891.2 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAPPC6A | NM_001270891.2 | c.*10G>A | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000585934.1 | NP_001257820.1 | ||
TRAPPC6A | NM_024108.3 | c.*10G>A | 3_prime_UTR_variant | Exon 6 of 6 | NP_077013.1 | |||
TRAPPC6A | NM_001270892.2 | c.*80G>A | 3_prime_UTR_variant | Exon 5 of 5 | NP_001257821.1 | |||
TRAPPC6A | NM_001270893.2 | c.*80G>A | 3_prime_UTR_variant | Exon 5 of 5 | NP_001257822.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0121 AC: 1839AN: 152120Hom.: 40 Cov.: 33
GnomAD3 exomes AF: 0.00337 AC: 842AN: 250140Hom.: 15 AF XY: 0.00259 AC XY: 351AN XY: 135474
GnomAD4 exome AF: 0.00122 AC: 1778AN: 1461576Hom.: 30 Cov.: 31 AF XY: 0.00106 AC XY: 770AN XY: 727106
GnomAD4 genome AF: 0.0121 AC: 1845AN: 152238Hom.: 40 Cov.: 33 AF XY: 0.0117 AC XY: 874AN XY: 74454
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