M-961-T-C

Variant names:

• chrM-961-T-C
• rs3888511
• ENST00000389680.2:n.314T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The ENST00000000000(RNR1):​n.314T>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 0.0091 (AC: 555)
• Consequence: RNR1 ENST00000000000 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1 DEAF+-possibly-LVNC-associated,DEAF-/-AD-associated-/-intellectual-disability,Possibly-DEAF-associated
• Conservation: PhyloP100: -7.53
• Publications: 13 publications found

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]

MT-RNR1 Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant M-961-T-C is Benign according to our data. Variant chrM-961-T-C is described in ClinVar as Benign. ClinVar VariationId is 42236.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: High frequency in mitomap database: 0.0091
• BS2: High AC in GnomadMitoHomoplasmic at 280

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000389680.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-RNR1	ENST00000389680.2	TSL:6	n.314T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

Mitomap GenBank AF: 0.0091 AC: 555

Gnomad homoplasmic AF: 0.0050 AC: 280 AN: 56400

Gnomad heteroplasmic AF: 0.00032 AC: 18 AN: 56400

Alfa AF: 0.0205 Hom.: 845

Mitomap

Disease(s): DEAF+-possibly-LVNC-associated,DEAF-/-AD-associated-/-intellectual-disability,Possibly-DEAF-associated

Status: Unclear,Unclear,Unclear

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-7.5

Other links and lift over

dbSNP: rs3888511; hg19: chrM-963;