M-956-C-T

Position:

• chrM-956-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Mitomap GenBank: 𝑓 0.00020 (AC: 12)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -5.51

Genes affected

RNR1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	unassigned_transcript_4786	n.309C>T		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: 0.00020 AC: 12

Gnomad homoplasmic AF: 0.000035 AC: 2 AN: 56419

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56419

Mitomap

No disease associated.

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jan 08, 2013

Variant classified as Uncertain Significance - Favor Benign. The 956C>T variant in MTRNR1 has not been identified by our laboratory but has been reported once i n a publically available database (http://mitolsdb.igib.res.in). Mitochondrial v ariants follow a maternal inheritance pattern. Although penetrance of mitochondr ial variants can be reduced, given the lack of reported family history of hearin g loss in this family and no data to support a pathogenic role, we would lean to wards a more likely benign role for this variant. However, a conclusive interpre tation is not possible. -

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: rs397515729; hg19: chrM-958;