rs397756552
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020751.3(COG6):c.624-3del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000406 in 1,390,130 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 21)
Exomes 𝑓: 0.00046 ( 0 hom. )
Consequence
COG6
NM_020751.3 splice_polypyrimidine_tract, intron
NM_020751.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.428
Genes affected
COG6 (HGNC:18621): (component of oligomeric golgi complex 6) This gene encodes a subunit of the conserved oligomeric Golgi complex that is required for maintaining normal structure and activity of the Golgi apparatus. The encoded protein is organized with conserved oligomeric Golgi complex components 5, 7 and 8 into a sub-complex referred to as lobe B. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COG6 | NM_020751.3 | c.624-3del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000455146.8 | |||
COG6 | NM_001145079.2 | c.624-3del | splice_polypyrimidine_tract_variant, intron_variant | ||||
COG6 | XM_011535168.2 | c.624-3del | splice_polypyrimidine_tract_variant, intron_variant | ||||
COG6 | NR_026745.1 | n.789-3del | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COG6 | ENST00000455146.8 | c.624-3del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_020751.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151474Hom.: 0 Cov.: 21
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GnomAD4 exome AF: 0.000455 AC: 564AN: 1238656Hom.: 0 Cov.: 20 AF XY: 0.000436 AC XY: 273AN XY: 626076
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at