rs398027674
Your query was ambiguous. Multiple possible variants found:
- chr15-65002962-CAAAAAAAAAAA-C
- chr15-65002962-CAAAAAAAAAAA-CA
- chr15-65002962-CAAAAAAAAAAA-CAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAAAAAA
- chr15-65002962-CAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_139242.4(MTFMT):c.*89_*99delTTTTTTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000016 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000011 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MTFMT
NM_139242.4 3_prime_UTR
NM_139242.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.35
Publications
0 publications found
Genes affected
MTFMT (HGNC:29666): (mitochondrial methionyl-tRNA formyltransferase) The protein encoded by this nuclear gene localizes to the mitochondrion, where it catalyzes the formylation of methionyl-tRNA. [provided by RefSeq, Jun 2011]
MTFMT Gene-Disease associations (from GenCC):
- combined oxidative phosphorylation defect type 15Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- Leigh syndromeInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- Leigh syndrome with leukodystrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_139242.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| MTFMT | TSL:1 MANE Select | c.*89_*99delTTTTTTTTTTT | 3_prime_UTR | Exon 9 of 9 | ENSP00000220058.4 | Q96DP5-1 | |||
| MTFMT | c.*89_*99delTTTTTTTTTTT | 3_prime_UTR | Exon 10 of 10 | ENSP00000571121.1 | |||||
| MTFMT | c.*89_*99delTTTTTTTTTTT | 3_prime_UTR | Exon 9 of 9 | ENSP00000571118.1 |
Frequencies
GnomAD3 genomes 0.0000165 AC: 1AN: 60766Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
60766
Hom.:
Cov.:
0
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: 0.0000113 AC: 3AN: 264998Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134524 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
3
AN:
264998
Hom.:
AF XY:
AC XY:
1
AN XY:
134524
show subpopulations
African (AFR)
AF:
AC:
0
AN:
6634
American (AMR)
AF:
AC:
1
AN:
5878
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5620
East Asian (EAS)
AF:
AC:
0
AN:
15418
South Asian (SAS)
AF:
AC:
0
AN:
10124
European-Finnish (FIN)
AF:
AC:
0
AN:
12770
Middle Eastern (MID)
AF:
AC:
0
AN:
1046
European-Non Finnish (NFE)
AF:
AC:
2
AN:
194320
Other (OTH)
AF:
AC:
0
AN:
13188
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
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
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>80
Age
GnomAD4 genome 0.0000165 AC: 1AN: 60766Hom.: 0 Cov.: 0 AF XY: 0.0000364 AC XY: 1AN XY: 27454 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
60766
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
27454
show subpopulations
African (AFR)
AF:
AC:
0
AN:
14370
American (AMR)
AF:
AC:
0
AN:
5018
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1806
East Asian (EAS)
AF:
AC:
0
AN:
1838
South Asian (SAS)
AF:
AC:
0
AN:
1724
European-Finnish (FIN)
AF:
AC:
0
AN:
1498
Middle Eastern (MID)
AF:
AC:
0
AN:
108
European-Non Finnish (NFE)
AF:
AC:
1
AN:
33114
Other (OTH)
AF:
AC:
0
AN:
760
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
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
Genome 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
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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