rs56489998

Variant names:

• chrM-663-A-G
• rs56489998
• unassigned_transcript_4785:n.16A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.029 (AC: 1765)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 Coronary-atherosclerosis-risk
• Conservation: PhyloP100: 0.114

Genes affected

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)

ACMG classification

Verdict is Benign. Variant got -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

Frequencies

GnomAD4 exome Cov.: 0

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap GenBank AF: 0.029 AC: 1765

Gnomad homoplasmic AF: 0.048 AC: 2681 AN: 56420

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56420

Mitomap

Coronary-atherosclerosis-risk

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

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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: rs56489998; hg19: chrM-665;