chrM-980-T-C

Position:

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:
𝑓 0.0097 ( AC: 590 )

Consequence

RNR1
non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1
No linked disesase in Mitomap

Conservation

PhyloP100: -8.54
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant M-980-T-C is Benign according to our data. Variant chrM-980-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 42237.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
High frequency in mitomap database: 0.0097
BS2
High AC in GnomadMitoHomoplasmic at 226

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RNR1unassigned_transcript_4786 use as main transcriptn.333T>C non_coding_transcript_exon_variant 1/1
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:
0.0097
AC:
590
Gnomad homoplasmic
AF:
0.0040
AC:
226
AN:
56421
Gnomad heteroplasmic
AF:
0.000071
AC:
4
AN:
56421

Mitomap

No disease associated.

ClinVar

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

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineJan 09, 2018m.980T>C in MTRNR1: This variant has been observed in 2/1642 patients with heari ng loss and was absent from 449 controls (Lu 2010). However, this variant is als o reported with similar frequencies in broad populations (LOVD database http://w ww.lovd.nl/2.0; mtDB http://www.mtdb.igp.uu.se; HmtDB http://www.hmtdb.uniba.it: 8080/hmdb). Moreover, this region of mitochondrial DNA is not conserved. Of note , mouse, Xenopus, Drosophila and E. coli have a C at this position (Conrad 2008) . In summary, there is no data to support a disease-associated role and the popu lation frequency suggests that this variant is likely benign. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs397515731; hg19: chrM-982; API