GeneBe

2-74135948-CTTTTTTT-CTTTTTTTTTTT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_212552.3(BOLA3):​c.259-294_259-291dupAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000045 ( 0 hom., cov: 0)

Consequence

BOLA3
NM_212552.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.489

Publications

0 publications found
Variant links:
Genes affected
BOLA3 (HGNC:24415): (bolA family member 3) This gene encodes a protein that plays an essential role in the production of iron-sulfur (Fe-S) clusters for the normal maturation of lipoate-containing 2-oxoacid dehydrogenases, and for the assembly of the mitochondrial respiratory chain complexes. Mutation in this gene has been associated with multiple mitochondrial dysfunctions syndrome-2. Two alternatively spliced transcript variants encoding different isoforms with distinct subcellular localization have been reported for this gene (PMID:21944046). [provided by RefSeq, Dec 2011]
BOLA3 Gene-Disease associations (from GenCC):
  • multiple mitochondrial dysfunctions syndrome 2
    Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BOLA3NM_212552.3 linkc.259-294_259-291dupAAAA intron_variant Intron 3 of 3 ENST00000327428.10 NP_997717.2 Q53S33-1
BOLA3NM_001035505.2 linkc.170-294_170-291dupAAAA intron_variant Intron 2 of 2 NP_001030582.1 Q53S33-2Q8N338

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BOLA3ENST00000327428.10 linkc.259-291_259-290insAAAA intron_variant Intron 3 of 3 1 NM_212552.3 ENSP00000331369.5 Q53S33-1

Frequencies

GnomAD3 genomes
AF:
0.0000445
AC:
6
AN:
134708
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000229
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000473
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000445
AC:
6
AN:
134692
Hom.:
0
Cov.:
0
AF XY:
0.0000311
AC XY:
2
AN XY:
64308
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
36362
American (AMR)
AF:
0.000229
AC:
3
AN:
13082
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3308
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4638
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4110
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
6774
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
254
European-Non Finnish (NFE)
AF:
0.0000473
AC:
3
AN:
63456
Other (OTH)
AF:
0.00
AC:
0
AN:
1842
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.49

Splicing

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

Publications

Other links and lift over

dbSNP: rs55654893; hg19: chr2-74363075; API