GeneBe

16-23445969-TAAAAAA-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_153603.4(COG7):​c.170-14_170-9delTTTTTT variant causes a 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 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.00

Publications

2 publications found
Variant links:
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]
COG7 Gene-Disease associations (from GenCC):
  • COG7-congenital disorder of glycosylation
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, G2P, Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COG7NM_153603.4 linkc.170-14_170-9delTTTTTT intron_variant Intron 1 of 16 ENST00000307149.10 NP_705831.1 P83436A0A0S2Z652
COG7XM_017023870.2 linkc.-26-14_-26-9delTTTTTT intron_variant Intron 1 of 16 XP_016879359.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COG7ENST00000307149.10 linkc.170-14_170-9delTTTTTT intron_variant Intron 1 of 16 1 NM_153603.4 ENSP00000305442.5 P83436

Frequencies

GnomAD3 genomes
Cov.:
25
GnomAD4 exome
AF:
0.00000220
AC:
3
AN:
1362972
Hom.:
0
AF XY:
0.00000295
AC XY:
2
AN XY:
678998
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
29976
American (AMR)
AF:
0.0000519
AC:
2
AN:
38562
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24648
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37726
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79316
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
41514
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5094
European-Non Finnish (NFE)
AF:
9.53e-7
AC:
1
AN:
1049488
Other (OTH)
AF:
0.00
AC:
0
AN:
56648
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0953088), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.392
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
25
Alfa
AF:
0.00
Hom.:
4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
4.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs71379679; hg19: chr16-23457290; API