rs28608480

Positions:

• chrM-12477-T-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP7 BS2

The ENST00000361567.2(MT-ND5):​c.141T>C​(p.Ser47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Mitomap GenBank: 𝑓 0.0050 (AC: 307)
• Consequence: MT-ND5 ENST00000361567.2 synonymous
• Clinical Significance: Not reported in ClinVar Possible-HCM-susceptibility
• Conservation: PhyloP100: 0.166

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]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP7: Synonymous conserved (PhyloP=0.166 with no splicing effect.
• BS2: High AC in GnomadMitoHomoplasmic at 303

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MT-ND5	ENST00000361567.2	c.141T>C	p.Ser47=	synonymous_variant	1/1			ENSP00000354813	P1

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;