6-32706960-C-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000422088.1(MTCO3P1):n.-5G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0227 in 152,254 control chromosomes in the GnomAD database, including 59 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 0.023 ( 59 hom., cov: 32)
Exomes 𝑓: 0.0078 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MTCO3P1
ENST00000422088.1 upstream_gene
ENST00000422088.1 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.592
Publications
12 publications found
Genes affected
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0774 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MTCO3P1 | ENST00000422088.1 | n.-5G>C | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes 0.0227 AC: 3451AN: 152136Hom.: 59 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3451
AN:
152136
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00781 AC: 1AN: 128Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 68 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
128
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
68
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
1
AN:
122
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
6
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0227 AC: 3454AN: 152254Hom.: 59 Cov.: 32 AF XY: 0.0226 AC XY: 1682AN XY: 74448 show subpopulations
GnomAD4 genome
AF:
AC:
3454
AN:
152254
Hom.:
Cov.:
32
AF XY:
AC XY:
1682
AN XY:
74448
show subpopulations
African (AFR)
AF:
AC:
434
AN:
41536
American (AMR)
AF:
AC:
273
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
66
AN:
3470
East Asian (EAS)
AF:
AC:
206
AN:
5190
South Asian (SAS)
AF:
AC:
406
AN:
4824
European-Finnish (FIN)
AF:
AC:
91
AN:
10600
Middle Eastern (MID)
AF:
AC:
13
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1897
AN:
68024
Other (OTH)
AF:
AC:
52
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
177
353
530
706
883
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
48
96
144
192
240
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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