dbSNP rs199474700: TRNP:p.Phe20Ser (chrM-15965-A-G) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000000000(TRNP):c.59T>C(p.Phe20Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. 3/3 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Mitomap GenBank:

𝑓 0.00020 ( AC: 12 )

Consequence

TRNP
ENST00000000000 missense

Scores

Mitotip

Benign

1.9

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Dopaminergic-nerve-cell-death-(PD)

Conservation

PhyloP100: 0.985

Publications

2 publications found

Variant links:

Genes affected

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

TRNP links:

MT-CYB (HGNC:7427): (mitochondrially encoded cytochrome b) Predicted to enable metal ion binding activity. Predicted to be involved in several processes, including electron transport coupled proton transport; response to cobalamin; and response to glucagon. Located in mitochondrion. Implicated in ovarian carcinoma and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]

MT-CYB 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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new If you want to explore the variant's impact on the transcript ENST00000000000, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP6

Variant M-15965-A-G is Benign according to our data. Variant chrM-15965-A-G is described in ClinVar as Benign. ClinVar VariationId is 9571.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomadMitoHomoplasmic at 17

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

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

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MT-TP	ENST00000387461.2	TSL:6	n.59T>C	non_coding_transcript_exon	Exon 1 of 1
MT-CYB	ENST00000361789.2	TSL:6	c.*78A>G	downstream_gene	N/A	ENSP00000354554.2	P00156
MT-TT	ENST00000387460.2	TSL:6	n.*12A>G	downstream_gene	N/A

Frequencies

Mitomap GenBank

AF:

0.00020

AC:

Gnomad homoplasmic

AF:

0.00030

AC:

AN:

56433

Gnomad heteroplasmic

AF:

0.0

AC:

AN:

56433

Alfa

AF:

0.000327

Hom.:

Mitomap

Disease(s): Dopaminergic-nerve-cell-death-(PD)

Status: Reported

Publication(s):

31965079

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

MELAS syndrome (1)

Parkinson disease, mitochondrial (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

Mitotip

Benign

1.9

Hmtvar

Benign

0.20

PhyloP100

0.98

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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