Genetic Variant TRNP:c.-165G>C (chrM-16188-C-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The ENST00000000000(TRNP):c.-165G>C variant causes a upstream gene 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 0.0090 ( AC: 550 )

Consequence

TRNP
ENST00000000000 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

No linked disesase in Mitomap

Conservation

PhyloP100: -4.89

Publications

5 publications found

Variant links:

Genes affected

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

TRNP links:

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

TRNT Gene-Disease associations (from GenCC):

mitochondrial disease
Inheritance: Mitochondrial Classification: MODERATE Submitted by: ClinGen

TRNT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BS1

High frequency in mitomap database: 0.009

BS2

High AC in GnomadMitoHomoplasmic at 25

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000387461.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MT-TP	ENST00000387461.2	TSL:6	n.-165G>C		upstream_gene	N/A
	MT-TT	ENST00000387460.2	TSL:6	n.*235C>G		downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.0090

AC:

550

Gnomad homoplasmic

AF:

0.00044

AC:

AN:

56429

Gnomad heteroplasmic

AF:

0.000071

AC:

AN:

56429

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-4.9

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Mitomap

ClinVar

Computational scores

Publications

Other links and lift over