M-1382-A-C

Position:

• chrM-1382-A-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The ENST00000389680.2(MT-RNR1):​n.735A>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 0.0031 (AC: 192)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 Longevity-/-T2D-susceptibility
• Conservation: PhyloP100: 2.13

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant M-1382-A-C is Benign according to our data. Variant chrM-1382-A-C is described in ClinVar as [Benign]. Clinvar id is 42214.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 37

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNR1	RNR1.1	n.735A>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.735A>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: 0.0031 AC: 192

Gnomad homoplasmic AF: 0.00066 AC: 37 AN: 56434

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56434

Alfa AF: 0.00169 Hom.: 59

Mitomap

Longevity-/-T2D-susceptibility

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

Sep 26, 2014

m.1120C>T in MTRNR1: This variant is not expected to have clinical significance because it has been found in the general population at a frequency of 0.5% (122/ 24187 human mitochondrial DNA sequences) with a haplogroup-specific frequency of 2.1% and 69.1% in two different Japanese clades (http://www.mitomap.org). Addit ionally, this variant is not significantly over represented in individuals with nonsyndromic hearing loss as it has been found in 43/1642 (2.6%) Chinese childre n (a proportion of whom have been exposed to aminoglycosides) as well as 9/449 ( 2.0%) Chinese controls (Lu 2010), suggesting that this variant is most likely no t involved in the observed hearing loss. -

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: rs111033358; hg19: chrM-1384;