16-19067673-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_016138.5(COQ7):c.9C>T(p.Cys3Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000822 in 1,460,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
COQ7
NM_016138.5 synonymous
NM_016138.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.198
Publications
0 publications found
Genes affected
COQ7 (HGNC:2244): (coenzyme Q7, hydroxylase) The protein encoded by this gene is similar to a mitochondrial di-iron containing hydroxylase in Saccharomyces cerevisiae that is involved with ubiquinone biosynthesis. Mutations in the yeast gene lead to slower development and longer life span. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 16-19067673-C-T is Benign according to our data. Variant chr16-19067673-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1949824.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.198 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_016138.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| COQ7 | NM_016138.5 | MANE Select | c.9C>T | p.Cys3Cys | synonymous | Exon 1 of 6 | NP_057222.2 | ||
| COQ7 | NM_001370490.1 | c.9C>T | p.Cys3Cys | synonymous | Exon 1 of 5 | NP_001357419.1 | |||
| COQ7-DT | NR_119379.1 | n.19G>A | non_coding_transcript_exon | Exon 1 of 4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| COQ7 | ENST00000321998.10 | TSL:1 MANE Select | c.9C>T | p.Cys3Cys | synonymous | Exon 1 of 6 | ENSP00000322316.5 | ||
| COQ7 | ENST00000568985.5 | TSL:2 | c.9C>T | p.Cys3Cys | synonymous | Exon 1 of 7 | ENSP00000456734.1 | ||
| COQ7 | ENST00000937633.1 | c.9C>T | p.Cys3Cys | synonymous | Exon 1 of 4 | ENSP00000607692.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.0000205 AC: 5AN: 243560 AF XY: 0.0000226 show subpopulations
GnomAD2 exomes
AF:
AC:
5
AN:
243560
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460370Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 726522 show subpopulations
GnomAD4 exome
AF:
AC:
12
AN:
1460370
Hom.:
Cov.:
30
AF XY:
AC XY:
7
AN XY:
726522
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33418
American (AMR)
AF:
AC:
3
AN:
44548
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26094
East Asian (EAS)
AF:
AC:
2
AN:
39646
South Asian (SAS)
AF:
AC:
5
AN:
86230
European-Finnish (FIN)
AF:
AC:
0
AN:
53010
Middle Eastern (MID)
AF:
AC:
0
AN:
5760
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1111372
Other (OTH)
AF:
AC:
1
AN:
60292
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1
2
2
3
4
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
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50-55
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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