rs28608480

Variant names:

• chrM-12477-T-C
• rs28608480
• unassigned_transcript_4815:c.141T>C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: 𝑓 0.0050 (AC: 307)
• Consequence: ND5 synonymous
• Clinical Significance: Not reported in ClinVar Possible-HCM-susceptibility
• Conservation: PhyloP100: 0.166

Genes affected

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]

TRNL2 (HGNC:7491): (mitochondrially encoded tRNA leucine 2 (CUN))

TRNS2 (HGNC:7498): (mitochondrially encoded tRNA serine 2 (AGU/C))

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomadMitoHomoplasmic at 303

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ND5	unassigned_transcript_4815	c.141T>C	p.Ser47Ser	synonymous_variant	Exon 1 of 1
TRNL2	unassigned_transcript_4814	c.*141T>C		downstream_gene_variant
TRNS2	unassigned_transcript_4813	c.*212T>C		downstream_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: 0.0050 AC: 307

Gnomad homoplasmic AF: 0.0054 AC: 303 AN: 56418

Gnomad heteroplasmic AF: 0.00012 AC: 7 AN: 56418

Alfa AF: 0.00275 Hom.: 13

Mitomap

Possible-HCM-susceptibility

ClinVar

Not reported in ClinVar

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: rs28608480; hg19: chrM-12478;