rs199474700

chrM-15965-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4 BP6_Moderate BS2

The ENST00000387461.2(MT-TP):n.59T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Mitomap GenBank: 𝑓 0.00020 (AC: 12)
• Consequence: MT-TP ENST00000387461.2 non_coding_transcript_exon
• Scores: Mitotip Benign 1.9
• Clinical Significance: Benign criteria provided, single submitter B:1 O:1 Dopaminergic-nerve-cell-death-(PD)
• Conservation: PhyloP100: 0.985

Genes affected

MT-TP (HGNC:7494): (mitochondrially encoded tRNA proline)

TRNP (HGNC:):

MT-TT (HGNC:7499): (mitochondrially encoded tRNA threonine)

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Mitotip and hmtvar scores support benign criterium.
• BP6: Variant M-15965-A-G is Benign according to our data. Variant chrM-15965-A-G is described in ClinVar as [Benign]. Clinvar id is 9571.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High AC in GnomadMitoHomoplasmic at 17

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRNP	TRNP.1	n.59T>C		non_coding_transcript_exon_variant	1/1
TRNT	TRNT.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-TP	ENST00000387461.2	n.59T>C		non_coding_transcript_exon_variant	1/1
MT-TT	ENST00000387460.2			downstream_gene_variant

Frequencies

GnomAD4 exome Cov.: 0

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

Mitomap GenBank AF: 0.00020 AC: 12

Gnomad homoplasmic AF: 0.00030 AC: 17 AN: 56433

Gnomad heteroplasmic AF: 0.0 AC: 0 AN: 56433

Mitomap

Dopaminergic-nerve-cell-death-(PD)

ClinVar

Significance: Benign

Submissions summary: Benign:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign:1

Benign, criteria provided, single submitter

clinical testing

Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine

Jul 12, 2019

The NC_012920.1:m.15965A>G variant in MT-TP gene is interpreted to be a Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS1, BS2, BP4 -

Parkinson disease, mitochondrial Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Apr 01, 1999

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mitotip	Benign	1.9
Hmtvar	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199474700; hg19: chrM-15966;