rs113173809
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_007357.3(COG2):āc.1014T>Cā(p.Asp338Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00571 in 1,611,642 control chromosomes in the GnomAD database, including 36 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 0.0041 ( 3 hom., cov: 32)
Exomes š: 0.0059 ( 33 hom. )
Consequence
COG2
NM_007357.3 synonymous
NM_007357.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.822
Genes affected
COG2 (HGNC:6546): (component of oligomeric golgi complex 2) This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi complex. The encoded protein specifically interacts with the USO1 vesicle docking protein and may be necessary for normal Golgi ribbon formation and trafficking of Golgi enzymes. Mutations of this gene are associated with abnormal glycosylation within the Golgi apparatus. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 1-230675112-T-C is Benign according to our data. Variant chr1-230675112-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 478370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.822 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00409 (623/152330) while in subpopulation NFE AF= 0.00683 (465/68036). AF 95% confidence interval is 0.00632. There are 3 homozygotes in gnomad4. There are 275 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COG2 | NM_007357.3 | c.1014T>C | p.Asp338Asp | synonymous_variant | 9/18 | ENST00000366669.9 | NP_031383.1 | |
COG2 | NM_001145036.2 | c.1014T>C | p.Asp338Asp | synonymous_variant | 9/18 | NP_001138508.1 | ||
COG2 | XM_047449445.1 | c.675T>C | p.Asp225Asp | synonymous_variant | 7/16 | XP_047305401.1 | ||
LOC107985358 | XR_001738517.1 | n.187A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00409 AC: 623AN: 152212Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00473 AC: 1178AN: 248910Hom.: 5 AF XY: 0.00496 AC XY: 667AN XY: 134528
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GnomAD4 exome AF: 0.00588 AC: 8575AN: 1459312Hom.: 33 Cov.: 30 AF XY: 0.00587 AC XY: 4260AN XY: 725812
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GnomAD4 genome AF: 0.00409 AC: 623AN: 152330Hom.: 3 Cov.: 32 AF XY: 0.00369 AC XY: 275AN XY: 74488
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | COG2: BP4, BP7, BS2 - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Congenital disorder of glycosylation, type IIq Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
COG2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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