NM_001033050.3:c.-327C>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001033050.3(MTERF2):c.-327C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,222 control chromosomes in the GnomAD database, including 33,886 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 0.66 ( 33857 hom., cov: 33)
Exomes 𝑓: 0.80 ( 29 hom. )
Consequence
MTERF2
NM_001033050.3 5_prime_UTR
NM_001033050.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.20
Publications
8 publications found
Genes affected
MTERF2 (HGNC:30779): (mitochondrial transcription termination factor 2) Enables DNA binding activity. Predicted to be involved in termination of mitochondrial transcription. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTERF2 | NM_001033050.3 | c.-327C>G | 5_prime_UTR_variant | Exon 1 of 3 | ENST00000240050.9 | NP_001028222.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.659 AC: 100123AN: 152008Hom.: 33829 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
100123
AN:
152008
Hom.:
Cov.:
33
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 AF: 0.802 AC: 77AN: 96Hom.: 29 Cov.: 0 AF XY: 0.828 AC XY: 53AN XY: 64 show subpopulations
GnomAD4 exome
AF:
AC:
77
AN:
96
Hom.:
Cov.:
0
AF XY:
AC XY:
53
AN XY:
64
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
1
AN:
2
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
2
East Asian (EAS)
AF:
AC:
3
AN:
4
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
2
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
67
AN:
82
Other (OTH)
AF:
AC:
3
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.536
Heterozygous variant carriers
0
2
4
5
7
9
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Hom
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 AF: 0.659 AC: 100201AN: 152126Hom.: 33857 Cov.: 33 AF XY: 0.657 AC XY: 48890AN XY: 74360 show subpopulations
GnomAD4 genome
AF:
AC:
100201
AN:
152126
Hom.:
Cov.:
33
AF XY:
AC XY:
48890
AN XY:
74360
show subpopulations
African (AFR)
AF:
AC:
20614
AN:
41486
American (AMR)
AF:
AC:
10810
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
1997
AN:
3470
East Asian (EAS)
AF:
AC:
3850
AN:
5144
South Asian (SAS)
AF:
AC:
3175
AN:
4826
European-Finnish (FIN)
AF:
AC:
7254
AN:
10596
Middle Eastern (MID)
AF:
AC:
198
AN:
294
European-Non Finnish (NFE)
AF:
AC:
50336
AN:
67990
Other (OTH)
AF:
AC:
1424
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1715
3430
5146
6861
8576
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
806
1612
2418
3224
4030
<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:
Asia WGS
AF:
AC:
2383
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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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