rs141205658
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_021942.6(TRAPPC11):c.1347G>A(p.Pro449=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,952 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 (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
TRAPPC11
NM_021942.6 synonymous
NM_021942.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0360
Genes affected
TRAPPC11 (HGNC:25751): (trafficking protein particle complex subunit 11) The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 4-183684204-G-A is Benign according to our data. Variant chr4-183684204-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 541351.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.036 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC11 | NM_021942.6 | c.1347G>A | p.Pro449= | synonymous_variant | 13/30 | ENST00000334690.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.1347G>A | p.Pro449= | synonymous_variant | 13/30 | 1 | NM_021942.6 | P1 | |
TRAPPC11 | ENST00000357207.8 | c.1347G>A | p.Pro449= | synonymous_variant | 13/31 | 1 | |||
TRAPPC11 | ENST00000512476.1 | c.165G>A | p.Pro55= | synonymous_variant | 2/19 | 1 | |||
TRAPPC11 | ENST00000505676.5 | c.348+198G>A | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251260Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135804
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GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461676Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727158
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type R18 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at