M-980-T-C

Position:

• chrM-980-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

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

• Frequency: Mitomap GenBank: 𝑓 0.0097 (AC: 590)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -8.54

Genes affected

RNR1 (HGNC:):

ACMG classification

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
RNR1	unassigned_transcript_4786	n.333T>C		non_coding_transcript_exon_variant	1/1

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

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jan 09, 2018

m.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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs397515731; hg19: chrM-982;