4-183679418-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_021942.6(TRAPPC11):c.897C>T(p.Ile299Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. I299I) has been classified as Benign.
Frequency
Consequence
NM_021942.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.897C>T | p.Ile299Ile | synonymous_variant | 9/30 | 1 | NM_021942.6 | ENSP00000335371.6 | ||
TRAPPC11 | ENST00000357207.8 | c.897C>T | p.Ile299Ile | synonymous_variant | 9/31 | 1 | ENSP00000349738.4 | |||
TRAPPC11 | ENST00000505676.5 | n.163-790C>T | intron_variant | 1 | ENSP00000422915.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249704Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135030
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460246Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726458
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type R18 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at