M-1442-G-A

Position:

• chrM-1442-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_Strong BS1 BS2

The ENST00000389680.2(MT-RNR1):​n.795G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency: Mitomap GenBank: 𝑓 0.0060 (AC: 364)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3 No linked disesase in Mitomap
• Conservation: PhyloP100: 0.166

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]

RNR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP6: Variant M-1442-G-A is Benign according to our data. Variant chrM-1442-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 42221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: High frequency in mitomap database: 0.006
• BS2: High AC in GnomadMitoHomoplasmic at 1600

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNR1	RNR1.1	n.795G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-RNR1	ENST00000389680.2	n.795G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.0060 AC: 364

Gnomad homoplasmic AF: 0.028 AC: 1600 AN: 56394

Gnomad heteroplasmic AF: 0.00012 AC: 7 AN: 56394

Alfa AF: 0.00255 Hom.: 89

Mitomap

No disease associated.

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 16, 2013	m.1442G>A in MTRNR1: This variant has been reported in 8% (10/120) of chromosom es from an African population sequenced by the 1000 Genome Project (dbSNP rs2835 8573). It has also been reported in broad populations at 1-4% frequency (LOVD da tabase http://www.lovd.nl/2.0; mtDB http://www.mtdb.igp.uu.se; HmtDB http://www. hmtdb.uniba.it:8080/hmdb) and belongs to the R7a'b haplotype group (http://www.f amilytreedna.com/mtDNA-Haplogroup-Mutations.aspx#). It has been identified in 3/ 1806 patients with hearing loss (0.2%) as well as in 4/675 controls (0.5%) (Li 2 004, Lu 2010). In summary, in the absence of any statistically significant assoc iation to hearing loss, the frequency of this variant suggests that it is likel y benign. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Athena Diagnostics

Nov 19, 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: rs28358573; hg19: chrM-1444;