rs111033325

Positions:

• chrM-1393-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_Strong BS2

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

• Frequency: Mitomap GenBank: 𝑓 0.0020 (AC: 120)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2 No linked disesase in Mitomap
• Conservation: PhyloP100: -3.52

Genes affected

RNR1 (HGNC:7470): (mitochondrially encoded 12S RNA) Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP6: Variant M-1393-G-A is Benign according to our data. Variant chrM-1393-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 42217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 103

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.746G>A		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: 0.0020 AC: 120

Gnomad homoplasmic AF: 0.0018 AC: 103 AN: 56421

Gnomad heteroplasmic AF: 0.000089 AC: 5 AN: 56421

Alfa AF: 0.000510 Hom.: 1

Mitomap

No disease associated.

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Aug 11, 2015

m.1393G>A in MT-RNR1: This variant is not expected to have clinical significance because it is a common variant across multiple haplotypes in a human phylogenet ic database (mito map database: mitomap.org). Although this variant has been ide ntified in 1 Saudi individual with Leber's hereditary optic neuropathy (LHON; A bu-Amero 2006) and 1 Chinese individual with aminoglycoside induced hearing loss (Lu 2010), it has been seen in 26/159 (16.3%) Saudi controls (Abu-Amero 2006) a nd has also been identified in the general population at a frequency of 0.16% (4 9/29867) human mitochondrial DNA sequences (mito map database: mitomap.org). -

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Dec 29, 2016

- -

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: rs111033325; hg19: chrM-1395;