chr17-73193103-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The NM_018714.3(COG1):c.34C>T(p.Arg12Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000298 in 1,611,518 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00031 ( 10 hom. )
Consequence
COG1
NM_018714.3 missense
NM_018714.3 missense
Scores
2
3
10
Clinical Significance
Conservation
PhyloP100: 1.44
Genes affected
COG1 (HGNC:6545): (component of oligomeric golgi complex 1) The protein encoded by this gene is one of eight proteins (Cog1-8) which form a Golgi-localized complex (COG) required for normal Golgi morphology and function. It is thought that this protein is required for steps in the normal medial and trans Golgi-associated processing of glycoconjugates and plays a role in the organization of the Golgi-localized complex. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0076636076).
BP6
?
Variant 17-73193103-C-T is Benign according to our data. Variant chr17-73193103-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 193397.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000164 (25/151982) while in subpopulation SAS AF= 0.00395 (19/4816). AF 95% confidence interval is 0.00258. There are 0 homozygotes in gnomad4. There are 17 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COG1 | NM_018714.3 | c.34C>T | p.Arg12Trp | missense_variant | 1/14 | ENST00000299886.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COG1 | ENST00000299886.9 | c.34C>T | p.Arg12Trp | missense_variant | 1/14 | 1 | NM_018714.3 | P1 | |
COG1 | ENST00000438720.7 | c.34C>T | p.Arg12Trp | missense_variant | 1/13 | 1 | |||
COG1 | ENST00000582587.2 | c.13C>T | p.Arg5Trp | missense_variant, NMD_transcript_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 151866Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000812 AC: 196AN: 241386Hom.: 0 AF XY: 0.00106 AC XY: 141AN XY: 132394
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GnomAD4 exome AF: 0.000312 AC: 455AN: 1459536Hom.: 10 Cov.: 35 AF XY: 0.000455 AC XY: 330AN XY: 726044
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 16, 2014 | - - |
COG1 congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 10, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
Sift4G
Benign
T;T
Polyphen
1.0
.;D
Vest4
MutPred
Loss of disorder (P = 0);Loss of disorder (P = 0);
MVP
MPC
1.8
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
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