rs17098211

Variant summary

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

The NM_025152.3(NUBPL):​c.694-482A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 179,470 control chromosomes in the GnomAD database, including 7,438 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 0.18 ( 7396 hom., cov: 32)
Exomes 𝑓: 0.018 ( 42 hom. )

Consequence

NUBPL
NM_025152.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00400
Variant links:
Genes affected
NUBPL (HGNC:20278): (NUBP iron-sulfur cluster assembly factor, mitochondrial) This gene encodes a member of the Mrp/NBP35 ATP-binding proteins family. The encoded protein is required for the assembly of the respiratory chain NADH dehydrogenase (complex I), an oligomeric enzymatic complex located in the inner mitochondrial membrane. Mutations in this gene cause mitochondrial complex I deficiency. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

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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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NUBPLNM_025152.3 linkuse as main transcriptc.694-482A>G intron_variant ENST00000281081.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NUBPLENST00000281081.12 linkuse as main transcriptc.694-482A>G intron_variant 1 NM_025152.3 P1Q8TB37-1

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27381
AN:
152096
Hom.:
7366
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.587
Gnomad AMI
AF:
0.138
Gnomad AMR
AF:
0.0887
Gnomad ASJ
AF:
0.0655
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0120
Gnomad FIN
AF:
0.00773
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.0129
Gnomad OTH
AF:
0.158
GnomAD4 exome
AF:
0.0176
AC:
480
AN:
27256
Hom.:
42
Cov.:
0
AF XY:
0.0175
AC XY:
249
AN XY:
14234
show subpopulations
Gnomad4 AFR exome
AF:
0.504
Gnomad4 AMR exome
AF:
0.0470
Gnomad4 ASJ exome
AF:
0.0619
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00973
Gnomad4 FIN exome
AF:
0.00425
Gnomad4 NFE exome
AF:
0.00729
Gnomad4 OTH exome
AF:
0.0216
GnomAD4 genome
AF:
0.180
AC:
27463
AN:
152214
Hom.:
7396
Cov.:
32
AF XY:
0.174
AC XY:
12986
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.588
Gnomad4 AMR
AF:
0.0886
Gnomad4 ASJ
AF:
0.0655
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0118
Gnomad4 FIN
AF:
0.00773
Gnomad4 NFE
AF:
0.0129
Gnomad4 OTH
AF:
0.157
Alfa
AF:
0.0479
Hom.:
1183
Bravo
AF:
0.205
Asia WGS
AF:
0.0410
AC:
143
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
3.2
DANN
Benign
0.80

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: rs17098211; hg19: chr14-32315195; API