rs727504505

Variant names:

• chrM-1008-A-G
• rs727504505
• ENST00000389680.2:n.361A>G

Your query was ambiguous. Multiple possible variants found:

• chrM-1008-A-G
• chrM-1008-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000389680.2(MT-RNR1):​n.361A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: 𝑓 0.00060 (AC: 34)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -3.47
• Publications: 2 publications found

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]

MT-RNR1 Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomadMitoHomoplasmic at 31

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.361A>G		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-RNR1	ENST00000389680.2	n.361A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

Mitomap GenBank AF: 0.00060 AC: 34

Gnomad homoplasmic AF: 0.00055 AC: 31 AN: 56428

Gnomad heteroplasmic AF: 0.000053 AC: 3 AN: 56428

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

May 15, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

1008A>G variant in MTRNR1: This variant has been reported at a similar frequency in individuals with hearing loss (0.2%; 1/466) and in controls (0.3%; 1/400) s upporting a benign role (Konings 2008). In addition, it has been reported in thr ee other individuals who were screened for phylogenetic studies (Palanichamy 200 4, Behar 2008a, Behar 2008b, MITOMAP: http://www.mitomap.org/MITOMAP). In summar y, there is no data to support a disease-associated role and the population freq uency suggests that this variant is likely benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-3.5

Other links and lift over

dbSNP: rs727504505; hg19: chrM-1010;