rs111033179

chrM-1005-T-C

Variant summary

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

The ENST00000389680.2(MT-RNR1):n.358T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.0044 (AC: 272)
• Consequence: MT-RNR1 ENST00000389680.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 DEAF
• Conservation: PhyloP100: -2.63

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant M-1005-T-C is Benign according to our data. Variant chrM-1005-T-C is described in ClinVar as [Benign]. Clinvar id is 42201.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 78

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNR1	RNR1.1	n.358T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-RNR1	ENST00000389680.2	n.358T>C		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: 0.0044 AC: 272

Gnomad homoplasmic AF: 0.0014 AC: 78 AN: 56423

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56423

Alfa AF: 0.00182 Hom.: 63

Mitomap

DEAF

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

Jun 11, 2013

m.1005T>C in MTRNR1: This variant has been identified in 3/128 (2.3%) Chinese pe diatric individuals with hearing loss, but there is no evidence that these indiv iduals had a maternal family history of hearing loss (Li Z 2005). In addition, t his variant has been reported to be a benign polymorphism on MitoMap (www.mitoma p.org) and has also been identified in 7/2703 individuals in the Human Mitochond rial Genome Database (www.genpat.uu.se/mtDB/). Six of the seven (86%) individual s who have ethnicity data from the Human Mitochondrial Genome Database (www.genp at.uu.se/mtDB/) are of Asian decent. No phenotypic information is available from this database. Furthermore, this variant has been associated with a specific ha plotype in the Chinese population (Kong 2004). In summary, we believe this data suggests that the 1005T>C variant is likely to be a benign variant in the Asian population without clinical significance. -

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: rs111033179; hg19: chrM-1007;