rs527236194

Variant names:

• chrM-15784-T-C
• rs527236194
• ENST00000361789.2:c.1038T>C

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP6_Moderate BP7 BA1

The ENST00000361789.2(MT-CYB):​c.1038T>C​(p.Pro346Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.033 (AC: 2012)
• Consequence: MT-CYB ENST00000361789.2 synonymous
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1 POAG---potential-for-association
• Conservation: PhyloP100: -7.84
• Publications: 14 publications found

Genes affected

MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

TRNT (HGNC:7499): (mitochondrially encoded tRNA threonine)

TRNP (HGNC:7494): (mitochondrially encoded tRNA proline)

TRNP Gene-Disease associations (from GenCC):

• MERRF syndrome

  Inheritance: Mitochondrial Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P
• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -11 ACMG points.

• BP6: Variant M-15784-T-C is Benign according to our data. Variant chrM-15784-T-C is described in ClinVar as Benign. ClinVar VariationId is 143899.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-7.84 with no splicing effect.
• BA1: High frequency in mitomap database: 0.032899998

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361789.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-CYB	ENST00000361789.2	TSL:6	c.1038T>C	p.Pro346Pro	synonymous	Exon 1 of 1	ENSP00000354554.2
	MT-TT	ENST00000387460.2	TSL:6	n.-104T>C		upstream_gene	N/A
	MT-TP	ENST00000387461.2	TSL:6	n.*172A>G		downstream_gene	N/A

Frequencies

Mitomap GenBank AF: 0.033 AC: 2012

Gnomad homoplasmic AF: 0.063 AC: 3527 AN: 56396

Gnomad heteroplasmic AF: 0.00012 AC: 7 AN: 56396

Alfa AF: 0.0421 Hom.: 2498

Mitomap

Disease(s): POAG---potential-for-association

Status: Reported

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	1	Familial cancer of breast (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-7.8
Mutation Taster		=57/43	polymorphism

Other links and lift over

dbSNP: rs527236194; hg19: chrM-15785;