rs111033322

Positions:

• chrM-1406-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 Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.0030 (AC: 183)
• Consequence: RNR1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -4.08

Genes affected

RNR1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant M-1406-T-C is Benign according to our data. Variant chrM-1406-T-C is described in ClinVar as [Benign]. Clinvar id is 42218.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 168

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	unassigned_transcript_4786	n.759T>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: 0.0030 AC: 183

Gnomad homoplasmic AF: 0.0030 AC: 168 AN: 56432

Gnomad heteroplasmic AF: 0.000035 AC: 2 AN: 56432

Alfa AF: 0.00485 Hom.: 168

Mitomap

No disease associated.

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Aug 18, 2010

This variant is classified as benign due to an equal frequency in cases and cont rols (Maca-Meyer 2001, Herrnstadt 2002, Mishmar 2003, Palanichamy 2004, Kivisild 2006, Pierson 2006, Konings 2008, Elstner 2008, Rydzanicz 2010, mtDB Online Dat abase). -

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: rs111033322; hg19: chrM-1408;