rs111033356

Positions:

• chrM-1420-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_Strong BS2

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

• Frequency: Mitomap GenBank: 𝑓 0.0021 (AC: 131)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 No linked disesase in Mitomap
• Conservation: PhyloP100: -0.923

Genes affected

RNR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP6: Variant M-1420-T-C is Benign according to our data. Variant chrM-1420-T-C is described in ClinVar as [Benign]. Clinvar id is 42219.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 199

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	unassigned_transcript_4786	n.773T>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: 0.0021 AC: 131

Gnomad homoplasmic AF: 0.0035 AC: 199 AN: 56423

Gnomad heteroplasmic AF: 0.000053 AC: 3 AN: 56423

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

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jun 26, 2017

m.1420T>C in MTRNR1: This variant is not expected to have clinical significance because it has been identified in 12.1% (55/456) of the L1c haplogroup in MitoMa p (https://www.mitomap.org). -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Athena Diagnostics

May 29, 2018

- -

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: rs111033356; hg19: chrM-1422;