rs28718242

Positions:

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP6_ModerateBP7BS1BS2

The ENST00000361381.2(MT-ND4):ā€‹c.1140T>Cā€‹(p.Ser380=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Mitomap GenBank:
š‘“ 0.0086 ( AC: 528 )

Consequence

MT-ND4
ENST00000361381.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -8.87
Variant links:
Genes affected
MT-ND4 (HGNC:7459): (mitochondrially encoded NADH dehydrogenase 4) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Parkinson's disease; macular degeneration; and schizophrenia. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP6
Variant M-11899-T-C is Benign according to our data. Variant chrM-11899-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 235318.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-8.87 with no splicing effect.
BS1
High frequency in mitomap database: 0.0086
BS2
High AC in GnomadMitoHomoplasmic at 585

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-ND4ENST00000361381.2 linkuse as main transcriptc.1140T>C p.Ser380= synonymous_variant 1/1 P1

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0086
AC:
528
Gnomad homoplasmic
AF:
0.010
AC:
585
AN:
56425
Gnomad heteroplasmic
AF:
0.000035
AC:
2
AN:
56425
Alfa
AF:
0.00352
Hom.:
131

Mitomap

No disease associated.

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCenter for Pediatric Genomic Medicine, Children's Mercy Hospital and ClinicsAug 12, 2015- -

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.

Other links and lift over

dbSNP: rs28718242; hg19: chrM-11900; API