rs702466

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_212552.3(BOLA3):​c.170-463G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,124 control chromosomes in the GnomAD database, including 9,425 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 9425 hom., cov: 33)

Consequence

BOLA3
NM_212552.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.427
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BOLA3NM_212552.3 linkuse as main transcriptc.170-463G>C intron_variant ENST00000327428.10
BOLA3NM_001035505.2 linkuse as main transcriptc.169+2366G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BOLA3ENST00000327428.10 linkuse as main transcriptc.170-463G>C intron_variant 1 NM_212552.3 P1Q53S33-1

Frequencies

GnomAD3 genomes
AF:
0.327
AC:
49738
AN:
152006
Hom.:
9423
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.146
Gnomad AMI
AF:
0.348
Gnomad AMR
AF:
0.317
Gnomad ASJ
AF:
0.404
Gnomad EAS
AF:
0.223
Gnomad SAS
AF:
0.215
Gnomad FIN
AF:
0.524
Gnomad MID
AF:
0.462
Gnomad NFE
AF:
0.420
Gnomad OTH
AF:
0.347
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.327
AC:
49749
AN:
152124
Hom.:
9425
Cov.:
33
AF XY:
0.328
AC XY:
24408
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.146
Gnomad4 AMR
AF:
0.317
Gnomad4 ASJ
AF:
0.404
Gnomad4 EAS
AF:
0.223
Gnomad4 SAS
AF:
0.216
Gnomad4 FIN
AF:
0.524
Gnomad4 NFE
AF:
0.419
Gnomad4 OTH
AF:
0.350
Alfa
AF:
0.376
Hom.:
1494
Bravo
AF:
0.305
Asia WGS
AF:
0.242
AC:
841
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.0
DANN
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs702466; hg19: chr2-74369950; API