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

Scores

Mitotip
Benign
3.0

Clinical Significance

Likely benign criteria provided, single submitter B:1
MELAS

Conservation

PhyloP100: 2.09
Variant links:
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
TRNVunassigned_transcript_4787 use as main transcriptc.39A>G p.Leu13Leu synonymous_variant 1/1
RNR2unassigned_transcript_4788 use as main transcriptn.-31A>G upstream_gene_variant
RNR1unassigned_transcript_4786 use as main transcriptn.*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
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0
AC:
2
Gnomad homoplasmic
AF:
0.000071
AC:
4
AN:
56431
Gnomad heteroplasmic
AF:
0.000018
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 submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineJul 12, 2019The 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G variant in MT-TV gene is interpreted to be a Likely Benign variant based on the modified ACMG guidelines (unpublished).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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
3.0
Hmtvar
Benign
0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1603218594; hg19: chrM-1642; API