M-14783-T-C

Variant names:

• chrM-14783-T-C
• rs193302982
• unassigned_transcript_4818:c.37T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.20 (AC: 12413)
• Consequence: CYTB synonymous
• Clinical Significance: Benign criteria provided, single submitter P:1 B:1 Possible-role-in-high-altitude-sickness
• Conservation: PhyloP100: 3.18

Genes affected

CYTB (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]

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)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant M-14783-T-C is Benign according to our data. Variant chrM-14783-T-C is described in ClinVar as [Benign]. Clinvar id is 140588.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: High frequency in mitomap database: 0.203

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYTB	unassigned_transcript_4818	c.37T>C	p.Leu13Leu	synonymous_variant	Exon 1 of 1
ND6	unassigned_transcript_4816	c.-110A>G		upstream_gene_variant
TRNE	unassigned_transcript_4817	c.-41A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.20 AC: 12413

Gnomad homoplasmic AF: 0.055 AC: 3118 AN: 56336

Gnomad heteroplasmic AF: 0.000053 AC: 3 AN: 56336

Alfa AF: 0.0205 Hom.: 168

Mitomap

Possible-role-in-high-altitude-sickness

ClinVar

Significance: Benign

Submissions summary: Pathogenic:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial cancer of breast Pathogenic:1 Benign:1

-

Department of Zoology Govt. MVM College

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Aug 29, 2023

Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: curation

Clinical significance based on ACMG v2.0 -

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: rs193302982; hg19: chrM-14784;