4-183666322-G-C
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_021942.6(TRAPPC11):āc.270G>Cā(p.Leu90Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,614,172 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0071 ( 11 hom., cov: 32)
Exomes š: 0.00072 ( 6 hom. )
Consequence
TRAPPC11
NM_021942.6 synonymous
NM_021942.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.92
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 -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 4-183666322-G-C is Benign according to our data. Variant chr4-183666322-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 474357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.92 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00714 (1088/152320) while in subpopulation AFR AF= 0.025 (1041/41564). AF 95% confidence interval is 0.0238. There are 11 homozygotes in gnomad4. There are 532 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAPPC11 | NM_021942.6 | c.270G>C | p.Leu90Leu | synonymous_variant | 3/30 | ENST00000334690.11 | NP_068761.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.270G>C | p.Leu90Leu | synonymous_variant | 3/30 | 1 | NM_021942.6 | ENSP00000335371.6 |
Frequencies
GnomAD3 genomes AF: 0.00714 AC: 1086AN: 152202Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00190 AC: 478AN: 251436Hom.: 5 AF XY: 0.00147 AC XY: 200AN XY: 135892
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GnomAD4 exome AF: 0.000718 AC: 1049AN: 1461852Hom.: 6 Cov.: 31 AF XY: 0.000612 AC XY: 445AN XY: 727228
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GnomAD4 genome AF: 0.00714 AC: 1088AN: 152320Hom.: 11 Cov.: 32 AF XY: 0.00714 AC XY: 532AN XY: 74492
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 16, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 01, 2021 | - - |
Autosomal recessive limb-girdle muscular dystrophy type R18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
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