19-45163230-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001270891.2(TRAPPC6A):c.449-7C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001270891.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAPPC6A | NM_001270891.2 | c.449-7C>G | splice_region_variant, intron_variant | Intron 5 of 5 | ENST00000585934.1 | NP_001257820.1 | ||
TRAPPC6A | NM_024108.3 | c.491-7C>G | splice_region_variant, intron_variant | Intron 5 of 5 | NP_077013.1 | |||
TRAPPC6A | NM_001270892.2 | c.*39-7C>G | splice_region_variant, intron_variant | Intron 4 of 4 | NP_001257821.1 | |||
TRAPPC6A | NM_001270893.2 | c.*39-7C>G | splice_region_variant, intron_variant | Intron 4 of 4 | NP_001257822.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249530Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135124
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461618Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727126
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at