rs2856982

Variant names:

• chrM-1018-G-A
• rs2856982
• ENST00000389680.2:n.371G>A

Your query was ambiguous. Multiple possible variants found:

• chrM-1018-G-A
• chrM-1018-G-T

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BA1

The ENST00000389680.2(MT-RNR1):​n.371G>A 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 0.072 (AC: 4409)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 No linked disesase in Mitomap
• Conservation: PhyloP100: -0.156
• Publications: 9 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: Benign. The variant received -16 ACMG points.

• BP6: Variant M-1018-G-A is Benign according to our data. Variant chrM-1018-G-A is described in ClinVar as Benign. ClinVar VariationId is 42203.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: High frequency in mitomap database: 0.0721

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.371G>A		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.371G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

Mitomap GenBank AF: 0.072 AC: 4409

Gnomad homoplasmic AF: 0.15 AC: 8503 AN: 56261

Gnomad heteroplasmic AF: 0.000018 AC: 1 AN: 56261

Alfa AF: 0.121 Hom.: 3935

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Jul 28, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

1018G>A in MTRNR1: This variant is not expected to have clinical signficance bec ause it is a haplogroup-specific polymorphism in mtDNA found in African populati ons. The MitoMap database reports this substitution as a polymophrism frequentl y reported in GenBank (GB frequency 1693, http://www.mitomap.org/bin/view.pl/Mai n/SearchAllele) and mtDB reports this variant at a frequency of 5.5% (150/2704 s equences, http://www.mtdb.igp.uu.se/index.html). -

not provided Benign:1

May 29, 2018

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.16

Other links and lift over

dbSNP: rs2856982; hg19: chrM-1020;