14-39159508-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001079537.2(TRAPPC6B):c.124C>T(p.Arg42Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,605,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001079537.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC6B | NM_001079537.2 | c.124C>T | p.Arg42Ter | stop_gained | 2/6 | ENST00000330149.10 | |
TRAPPC6B | NM_177452.4 | c.124C>T | p.Arg42Ter | stop_gained | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC6B | ENST00000330149.10 | c.124C>T | p.Arg42Ter | stop_gained | 2/6 | 1 | NM_001079537.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000810 AC: 2AN: 246868Hom.: 0 AF XY: 0.00000748 AC XY: 1AN XY: 133622
GnomAD4 exome AF: 0.0000193 AC: 28AN: 1453010Hom.: 0 Cov.: 29 AF XY: 0.0000124 AC XY: 9AN XY: 722906
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74366
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 26, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at