rs190478555
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_021942.6(TRAPPC11):c.1287+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,612,732 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00095 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0014 ( 4 hom. )
Consequence
TRAPPC11
NM_021942.6 intron
NM_021942.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.304
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 Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 4-183684064-G-A is Benign according to our data. Variant chr4-183684064-G-A is described in ClinVar as [Benign]. Clinvar id is 474345.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-183684064-G-A is described in Lovd as [Likely_benign].
BS2
?
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC11 | NM_021942.6 | c.1287+10G>A | intron_variant | ENST00000334690.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.1287+10G>A | intron_variant | 1 | NM_021942.6 | P1 | |||
TRAPPC11 | ENST00000357207.8 | c.1287+10G>A | intron_variant | 1 | |||||
TRAPPC11 | ENST00000512476.1 | c.105+10G>A | intron_variant | 1 | |||||
TRAPPC11 | ENST00000505676.5 | c.348+58G>A | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000947 AC: 144AN: 152118Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00131 AC: 328AN: 251244Hom.: 0 AF XY: 0.00133 AC XY: 180AN XY: 135810
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GnomAD4 exome AF: 0.00136 AC: 1984AN: 1460496Hom.: 4 Cov.: 30 AF XY: 0.00137 AC XY: 999AN XY: 726666
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GnomAD4 genome ? AF: 0.000946 AC: 144AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.000779 AC XY: 58AN XY: 74450
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ClinVar
Significance: 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at