ENST00000361789.2:c.165C>T

Variant names:

• chrM-14911-C-T
• rs28357683
• ENST00000361789.2:c.165C>T

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.165C>T​(p.Tyr55Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.010 (AC: 628)
• Consequence: MT-CYB ENST00000361789.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1 No linked disesase in Mitomap
• Conservation: PhyloP100: -2.19
• Publications: 5 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]

MT-ND6 (HGNC:7462): (mitochondrially encoded NADH dehydrogenase 6) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Predicted to be located in mitochondrial inner membrane. Implicated in Leber hereditary optic neuropathy; Leigh disease; and spinal muscular atrophy with lower extremity predominante 2B. [provided by Alliance of Genome Resources, Apr 2022]

TRNE (HGNC:7479): (mitochondrially encoded tRNA glutamic acid)

TRNE Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: Mitochondrial Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

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

• BP6: Variant M-14911-C-T is Benign according to our data. Variant chrM-14911-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 235655.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.19 with no splicing effect.
• BA1: High frequency in mitomap database: 0.010299999

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYTB	unassigned_transcript_4818	c.165C>T	p.Tyr55Tyr	synonymous_variant	Exon 1 of 1
ND6	unassigned_transcript_4816	c.-238G>A		upstream_gene_variant
TRNE	unassigned_transcript_4817	c.-169G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MT-CYB	ENST00000361789.2	c.165C>T	p.Tyr55Tyr	synonymous_variant	Exon 1 of 1	6		ENSP00000354554.2
MT-ND6	ENST00000361681.2	c.-238G>A		upstream_gene_variant		6		ENSP00000354665.2
MT-TE	ENST00000387459.1	n.-169G>A		upstream_gene_variant		6

Frequencies

Mitomap GenBank AF: 0.010 AC: 628

Gnomad homoplasmic AF: 0.026 AC: 1476 AN: 56415

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56415

Alfa AF: 0.0204 Hom.: 330

Mitomap

No disease associated.

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 12, 2015

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.2

Other links and lift over

dbSNP: rs28357683; hg19: chrM-14912;