M-1640-A-G
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS2
Variant has been reported in ClinVar as Likely benign (★).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 2 )
Consequence
TRNV
synonymous
synonymous
Scores
Mitotip
Benign
Clinical Significance
MELAS
Conservation
PhyloP100: 2.09
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very low frequency in mitomap database: 0.0
BP6
Variant M-1640-A-G is Benign according to our data. Variant chrM-1640-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 689844.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomadMitoHomoplasmic at 4
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNV | unassigned_transcript_4787 use as main transcript | c.39A>G | p.Leu13Leu | synonymous_variant | 1/1 | |||
RNR2 | unassigned_transcript_4788 use as main transcript | n.-31A>G | upstream_gene_variant | |||||
RNR1 | unassigned_transcript_4786 use as main transcript | n.*39A>G | downstream_gene_variant | |||||
use as main transcript |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
2
Gnomad homoplasmic
AF:
AC:
4
AN:
56431
Gnomad heteroplasmic
AF:
AC:
1
AN:
56431
Mitomap
MELAS
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MELAS syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Jul 12, 2019 | The NC_012920.1:m.1640A>G variant in MT-TV gene is interpreted to be a Likely Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS4, BP4, BP5 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at