M-12477-T-C

Position:

chrM-12477-T-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

Scores

Clinical Significance

Not reported in ClinVar

Possible-HCM-susceptibility

Conservation

PhyloP100: 0.166

Variant links:

Genes affected

ND5 (HGNC:):

ND5 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomadMitoHomoplasmic at 303

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ND5	unassigned_transcript_4816 use as main transcript	c.141T>C	p.Ser47Ser	synonymous_variant	1/1
	use as main transcript

Ensembl

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

Frequencies

GnomAD4 exome

Cov.:

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:

AN:

56418

Alfa

AF:

0.00275

Hom.:

Mitomap

Possible-HCM-susceptibility

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.