rs71379679
Positions:
- chr16-23445969-TAAAAAA-T
- chr16-23445969-TAAAAAA-TAA
- chr16-23445969-TAAAAAA-TAAA
- chr16-23445969-TAAAAAA-TAAAA
- chr16-23445969-TAAAAAA-TAAAAA
- chr16-23445969-TAAAAAA-TAAAAAAA
- chr16-23445969-TAAAAAA-TAAAAAAAA
- chr16-23445969-TAAAAAA-TAAAAAAAAA
- chr16-23445969-TAAAAAA-TAAAAAAAAAA
- chr16-23445969-TAAAAAA-TAAAAAAAAAAA
- chr16-23445969-TAAAAAA-TAAAAAAAAAAAA
- chr16-23445969-TAAAAAA-TAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_153603.4(COG7):c.170-14_170-9del variant causes a splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0000022 in 1,362,972 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: not found (cov: 25)
Exomes 𝑓: 0.0000022 ( 0 hom. )
Consequence
COG7
NM_153603.4 splice_polypyrimidine_tract, intron
NM_153603.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.00
Genes affected
COG7 (HGNC:18622): (component of oligomeric golgi complex 7) The protein encoded by this gene resides in the golgi, and constitutes one of the 8 subunits of the conserved oligomeric Golgi (COG) complex, which is required for normal golgi morphology and localization. Mutations in this gene are associated with the congenital disorder of glycosylation type IIe.[provided by RefSeq, May 2010]
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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 |
---|---|---|---|---|---|---|---|
COG7 | NM_153603.4 | c.170-14_170-9del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000307149.10 | |||
COG7 | XM_017023870.2 | c.-26-14_-26-9del | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COG7 | ENST00000307149.10 | c.170-14_170-9del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_153603.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD3 genomes
?
Cov.:
25
GnomAD4 exome AF: 0.00000220 AC: 3AN: 1362972Hom.: 0 AF XY: 0.00000295 AC XY: 2AN XY: 678998
GnomAD4 exome
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AC:
3
AN:
1362972
Hom.:
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AC XY:
2
AN XY:
678998
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GnomAD4 genome ? Cov.: 25
GnomAD4 genome
?
Cov.:
25
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at