Variant rs199474819 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The ENST00000387416.2(MT-TS1):n.42_43insG variant causes a non coding transcript exon 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:

Absent

Consequence

MT-TS1
ENST00000387416.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

No linked disesase in Mitomap

Conservation

PhyloP100: -1.71

Variant links:

Genes affected

MT-TS1 (HGNC:7497): (mitochondrially encoded tRNA serine 1 (UCN))

MT-TS1 links:

TRNS1 (HGNC:):

TRNS1 links:

MT-CO1 (HGNC:7419): (mitochondrially encoded cytochrome c oxidase I) Contributes to cytochrome-c oxidase activity. Predicted to be involved in electron transport coupled proton transport and mitochondrial electron transport, cytochrome c to oxygen. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]

MT-CO1 links:

MT-TD (HGNC:7478): (mitochondrially encoded tRNA aspartic acid)

MT-TD links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

No frequency data in Mitomap. Probably very rare.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
TRNS1	TRNS1.1 use as main transcript	n.42_43insG	non_coding_transcript_exon_variant	1/1
COX1	COX1.1 use as main transcript		downstream_gene_variant
TRND	TRND.1 use as main transcript		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	Appris
MT-TS1	ENST00000387416.2 linkuse as main transcript	n.42_43insG	non_coding_transcript_exon_variant	1/1
MT-CO1	ENST00000361624.2 linkuse as main transcript		downstream_gene_variant		P1
MT-TD	ENST00000387419.1 linkuse as main transcript		upstream_gene_variant

Frequencies

GnomAD4 exome

Cov.:

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

Mitomap

No disease associated.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.