rs56489998

Variant names:

• chrM-663-A-G
• rs56489998
• ENST00000389680.2:n.16A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000000000(RNR1):​n.16A>G 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 0.029 (AC: 1765)
• Consequence: RNR1 ENST00000000000 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 Coronary-atherosclerosis-risk
• Conservation: PhyloP100: 0.114
• Publications: 6 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]

TRNF (HGNC:7481): (mitochondrially encoded tRNA phenylalanine)

TRNF Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen
• MERRF syndrome

  Inheritance: Mitochondrial Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant M-663-A-G is Benign according to our data. Variant chrM-663-A-G is described in ClinVar as [Benign]. Clinvar id is 805059.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: High frequency in mitomap database: 0.028900001

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.16A>G		non_coding_transcript_exon_variant	Exon 1 of 1
TRNF	unassigned_transcript_4784	c.*16A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-RNR1	ENST00000389680.2	n.16A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
MT-TF	ENST00000387314.1	n.*16A>G		downstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.029 AC: 1765

Gnomad homoplasmic AF: 0.048 AC: 2681 AN: 56420

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56420

Alfa AF: 0.0581 Hom.: 681

Mitomap

Disease(s): Coronary-atherosclerosis-risk

Status: Reported

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 12, 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		0.11
Mutation Taster		=87/13	polymorphism

Other links and lift over

dbSNP: rs56489998; hg19: chrM-665;