rs2853518

Variant names:

• chrM-750-A-G
• rs2853518
• ENST00000389680.2:n.103A>G

Variant summary

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

The ENST00000000000(RNR1):​n.103A>G variant causes a non coding transcript exon change. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.98 (AC: 60110)
• Consequence: RNR1 ENST00000000000 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 O:2 No linked disesase in Mitomap
• Conservation: PhyloP100: 6.91
• Publications: 10 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-750-A-G is Benign according to our data. Variant chrM-750-A-G is described in ClinVar as [Benign]. Clinvar id is 441148.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: High frequency in mitomap database: 0.9832

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNR1	unassigned_transcript_4785	n.103A>G		non_coding_transcript_exon_variant	Exon 1 of 1
TRNF	unassigned_transcript_4784	c.*103A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-RNR1	ENST00000389680.2	n.103A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
MT-TF	ENST00000387314.1	n.*103A>G		downstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.98 AC: 60110

Gnomad homoplasmic AF: 0.98 AC: 55419 AN: 56354

Gnomad heteroplasmic AF: 0.00011 AC: 6 AN: 56354

Alfa AF: 0.970 Hom.: 7297

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Benign:1 Other:2

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Venous thromboembolism Other:1

-

Genomics Division, Defence Institute of Physiology and Allied Sciences

Significance: association not found

Review Status: no assertion criteria provided

Collection Method: case-control

Three age and sex matched study groups were taken and whole exome sequencing was performed. 1. Healthy Subjects (n=19) 2. Sea Level Venous Thromboembolism (n=15) 3. High Altitude Venous Thromboembolism (n=6). Nature of this variant is not provided. After analysis, it was found that rs2853518 is present in all study groups. First time it is being reported that there is association of rs28535138 with Venous thromboembolism. -

not provided Other:1

-

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.9

Other links and lift over

dbSNP: rs2853518; hg19: chrM-752;