rs111033323

chrM-1107-T-C

Variant summary

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

The ENST00000389680.2(MT-RNR1):n.460T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.0068 (AC: 417)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -0.822

Genes affected

MT-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]

RNR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant M-1107-T-C is Benign according to our data. Variant chrM-1107-T-C is described in ClinVar as [Benign]. Clinvar id is 42207.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: High frequency in mitomap database: 0.0068
• BS2: High AC in GnomadMitoHomoplasmic at 84

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNR1	RNR1.1	n.460T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-RNR1	ENST00000389680.2	n.460T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD4 exome Cov.: 0

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank AF: 0.0068 AC: 417

Gnomad homoplasmic AF: 0.0015 AC: 84 AN: 56426

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56426

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jun 08, 2012

1107T>C in MTRNR1: This variant is not expected to have clinical significance as it is common and at similar afrequencies in individuals with hearing loss and i n controls (Li 2005, Tang 2007, Bilal 2008, Lu 2010, http://www.mtdb.igp.uu.se). Moreover, this region of mitochondrial DNA is not evolutionarily conserved (Lu 2010) and this variant is part of known polymorphisms associated with mitochond rial haplogroups (Tanaka 2004, Lu 2010). In summary, there is no clear data to s upport a disease-associated role or risk for ototoxicity and the population freq uency of the variant suggests that it is 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: rs111033323; hg19: chrM-1109;