rs727503165

Positions:

• chrM-990-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.00060 (AC: 36)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1 DEAF
• Conservation: PhyloP100: -0.650

Genes affected

RNR1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant M-990-T-C is Benign according to our data. Variant chrM-990-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 163989.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 85

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	unassigned_transcript_4786	n.343T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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: 0.00060 AC: 36

Gnomad homoplasmic AF: 0.0015 AC: 85 AN: 56429

Gnomad heteroplasmic AF: 0.000053 AC: 3 AN: 56429

Mitomap

DEAF

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Dec 13, 2013

m.990T>C in MT-RNR1: The m.990T>C variant has been previously reported in 2/908 (0.2%) individuals with hearing loss and was not detected in 849 controls in tho se studies (Konings 2008, Shen 2011). However, it has been identified in 1.89% ( 19/1008) of individuals from broad populations by several human phylogeny studie s (MitoMap.org). Therefore, in the absence of any statistically significant asso ciation to hearing loss, the frequency of this variant in the general population , as evidenced by the phylogeny studies, suggests that it is likely benign. -

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: rs727503165; hg19: chrM-992;