M-1607-T-C

Position:

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:
𝑓 0.00020 ( AC: 12 )

Consequence

TRNV
synonymous

Scores

Mitotip
Benign
6.8

Clinical Significance

Benign criteria provided, single submitter B:1
Suspected-mito-disease

Conservation

PhyloP100: -1.71
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6
Variant M-1607-T-C is Benign according to our data. Variant chrM-1607-T-C is described in ClinVar as [Benign]. Clinvar id is 689833.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomadMitoHomoplasmic at 21

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRNVunassigned_transcript_4787 use as main transcriptc.6T>C p.Ser2Ser synonymous_variant 1/1
RNR1unassigned_transcript_4786 use as main transcriptn.*6T>C 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:
0.00020
AC:
12
Gnomad homoplasmic
AF:
0.00037
AC:
21
AN:
56428
Gnomad heteroplasmic
AF:
0.000035
AC:
2
AN:
56428

Mitomap

Suspected-mito-disease

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

MELAS syndrome Benign:1
Benign, criteria provided, single submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineJul 12, 2019The NC_012920.1:m.1607T>C variant in MT-TV gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
6.8
Hmtvar
Benign
0.10

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: rs1603218581; hg19: chrM-1609; API