chr2-3387868-C-CGGGCGACCT
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_016030.6(TRAPPC12):c.250_258dup(p.Asp84_Gly86dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000646 in 1,593,306 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000065 ( 0 hom. )
Consequence
TRAPPC12
NM_016030.6 inframe_insertion
NM_016030.6 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.68
Genes affected
TRAPPC12 (HGNC:24284): (trafficking protein particle complex subunit 12) Involved in several processes, including endoplasmic reticulum to Golgi vesicle-mediated transport; positive regulation of protein localization to kinetochore; and regulation of kinetochore assembly. Located in Golgi apparatus; kinetochore; and nucleoplasm. Part of TRAPP complex. Colocalizes with endoplasmic reticulum-Golgi intermediate compartment and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_016030.6.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC12 | NM_016030.6 | c.250_258dup | p.Asp84_Gly86dup | inframe_insertion | 2/12 | ENST00000324266.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC12 | ENST00000324266.10 | c.250_258dup | p.Asp84_Gly86dup | inframe_insertion | 2/12 | 1 | NM_016030.6 | P1 | |
TRAPPC12 | ENST00000382110.6 | c.250_258dup | p.Asp84_Gly86dup | inframe_insertion | 2/12 | 2 | P1 | ||
TRAPPC12 | ENST00000482645.1 | n.411_419dup | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152170Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000303 AC: 7AN: 230746Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 125344
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GnomAD4 exome AF: 0.0000652 AC: 94AN: 1441020Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 48AN XY: 713802
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GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74464
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 14, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at