rs3014960
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_031431.4(COG3):c.1491G>A(p.Gln497=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.888 in 1,529,194 control chromosomes in the GnomAD database, including 604,205 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.90 ( 61673 hom., cov: 32)
Exomes 𝑓: 0.89 ( 542532 hom. )
Consequence
COG3
NM_031431.4 splice_region, synonymous
NM_031431.4 splice_region, synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.57
Genes affected
COG3 (HGNC:18619): (component of oligomeric golgi complex 3) This gene encodes a component of the conserved oligomeric Golgi (COG) complex which is composed of eight different subunits and is required for normal Golgi morphology and localization. Defects in the COG complex result in multiple deficiencies in protein glycosylation. The protein encoded by this gene is involved in ER-Golgi transport.[provided by RefSeq, Jun 2011]
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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=-0.43).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COG3 | NM_031431.4 | c.1491G>A | p.Gln497= | splice_region_variant, synonymous_variant | 14/23 | ENST00000349995.10 | |
COG3 | XM_047430702.1 | c.1491G>A | p.Gln497= | splice_region_variant, synonymous_variant | 14/19 | ||
COG3 | XR_007063702.1 | n.1428G>A | splice_region_variant, non_coding_transcript_exon_variant | 13/14 | |||
COG3 | XR_429222.5 | n.1589G>A | splice_region_variant, non_coding_transcript_exon_variant | 14/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COG3 | ENST00000349995.10 | c.1491G>A | p.Gln497= | splice_region_variant, synonymous_variant | 14/23 | 1 | NM_031431.4 | P1 | |
COG3 | ENST00000465942.1 | n.466G>A | splice_region_variant, non_coding_transcript_exon_variant | 5/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.899 AC: 136753AN: 152112Hom.: 61613 Cov.: 32
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GnomAD3 exomes AF: 0.893 AC: 224020AN: 250776Hom.: 100159 AF XY: 0.892 AC XY: 120843AN XY: 135540
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GnomAD4 exome AF: 0.887 AC: 1221608AN: 1376964Hom.: 542532 Cov.: 21 AF XY: 0.888 AC XY: 612582AN XY: 690056
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GnomAD4 genome ? AF: 0.899 AC: 136872AN: 152230Hom.: 61673 Cov.: 32 AF XY: 0.899 AC XY: 66882AN XY: 74414
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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