M-16188-C-G

Variant names:

• chrM-16188-C-G
• rs55749223
• unassigned_transcript_4820:c.-165G>C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

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

• Frequency: Mitomap GenBank: 𝑓 0.0090 (AC: 550)
• Consequence: TRNP upstream_gene
• Clinical Significance: Not reported in ClinVar No linked disesase in Mitomap
• Conservation: PhyloP100: -4.89

Genes affected

TRNP (HGNC:7494): (mitochondrially encoded tRNA proline)

TRNT (HGNC:7499): (mitochondrially encoded tRNA threonine)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: High frequency in mitomap database: 0.009
• BS2: High AC in GnomadMitoHomoplasmic at 25

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRNP	unassigned_transcript_4820	c.-165G>C		upstream_gene_variant
TRNT	unassigned_transcript_4819	c.*235C>G		downstream_gene_variant

Ensembl

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

Frequencies

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

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

Mitomap GenBank AF: 0.0090 AC: 550

Gnomad homoplasmic AF: 0.00044 AC: 25 AN: 56429

Gnomad heteroplasmic AF: 0.000071 AC: 4 AN: 56429

Mitomap

No disease associated.

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: rs55749223; hg19: chrM-16190;