M-1617-C-T

Position:

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate

The ENST00000387342.1(MT-TV):​n.16C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Mitomap GenBank:
𝑓 0.0 ( AC: 2 )

Consequence

MT-TV
ENST00000387342.1 non_coding_transcript_exon

Scores

Mitotip
Benign
6.8

Clinical Significance

Likely benign criteria provided, single submitter B:1
No linked disesase in Mitomap

Conservation

PhyloP100: -1.84
Variant links:
Genes affected
MT-TV (HGNC:7500): (mitochondrially encoded tRNA valine)
MT-RNR1 (HGNC:7470): (mitochondrially encoded 12S RNA) Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very low frequency in mitomap database: 0.0
BP4
Mitotip and hmtvar scores support benign criterium.
BP6
Variant M-1617-C-T is Benign according to our data. Variant chrM-1617-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 689835.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRNVTRNV.1 use as main transcriptn.16C>T non_coding_transcript_exon_variant 1/1
RNR1RNR1.1 use as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-TVENST00000387342.1 linkuse as main transcriptn.16C>T non_coding_transcript_exon_variant 1/1
MT-RNR1ENST00000389680.2 linkuse as main transcript 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:
0.0
AC:
2
Gnomad homoplasmic
AF:
0.000035
AC:
2
AN:
56434
Gnomad heteroplasmic
AF:
0.0
AC:
0
AN:
56434

Mitomap

No disease associated.

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Benign:1
Likely benign, criteria provided, single submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineJul 12, 2019The NC_012920.1:m.1617C>T variant in MT-TV gene is interpreted to be a Likely Benign variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: BS4, BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mitotip
Benign
6.8
Hmtvar
Benign
0.0

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.

Other links and lift over

dbSNP: rs1603218583; hg19: chrM-1619; API