rs2853499

Positions:

• chrM-12372-G-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP6_Very_Strong BP7 BA1

The ENST00000361567.2(MT-ND5):​c.36G>A​(p.Leu12=) 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 0.14 (AC: 8474)
• Consequence: MT-ND5 ENST00000361567.2 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 Altered-brain-pH-/-sCJD-patients
• Conservation: PhyloP100: -5.07

Genes affected

MT-ND5 (HGNC:7461): (mitochondrially encoded NADH dehydrogenase 5) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and MELAS syndrome. [provided by Alliance of Genome Resources, Apr 2022]

MT-TL2 (HGNC:7491): (mitochondrially encoded tRNA leucine 2 (CUN))

TRNL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -17 ACMG points.

• BP6: Variant M-12372-G-A is Benign according to our data. Variant chrM-12372-G-A is described in ClinVar as [Benign]. Clinvar id is 522717.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-5.07 with no splicing effect.
• BA1: High frequency in mitomap database: 0.13859999

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRNL2	TRNL2.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-ND5	ENST00000361567.2	c.36G>A	p.Leu12=	synonymous_variant	1/1			P1
MT-TL2	ENST00000387456.1			downstream_gene_variant

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.14 AC: 8474

Gnomad homoplasmic AF: 0.16 AC: 8901 AN: 56353

Gnomad heteroplasmic AF: 0.00014 AC: 8 AN: 56353

Alfa AF: 0.259 Hom.: 1173

Mitomap

Altered-brain-pH-/-sCJD-patients

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

Mitochondrial disease Benign:1

Benign, criteria provided, single submitter

clinical testing

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Jul 20, 2024

- -

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: rs2853499; hg19: chrM-12373;