rs41419549

Positions:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Mitomap GenBank:
𝑓 0.0074 ( AC: 452 )

Consequence

ND2
synonymous

Scores

Clinical Significance

Not reported in ClinVar
No linked disesase in Mitomap

Conservation

PhyloP100: -4.82
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
High frequency in mitomap database: 0.0074
BS2
High AC in GnomadMitoHomoplasmic at 593

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ND2unassigned_transcript_4794 use as main transcriptc.535T>C p.Leu179Leu synonymous_variant 1/1
use as main transcript

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0074
AC:
452
Gnomad homoplasmic
AF:
0.011
AC:
593
AN:
56418
Gnomad heteroplasmic
AF:
0.000053
AC:
3
AN:
56418
Alfa
AF:
0.0117
Hom.:
55

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.

Other links and lift over

dbSNP: rs41419549; hg19: chrM-5005; API