chr14-31562039-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_025152.3(NUBPL):c.109-29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 1,549,298 control chromosomes in the GnomAD database, including 2,033 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.035 ( 124 hom., cov: 32)
Exomes 𝑓: 0.048 ( 1909 hom. )
Consequence
NUBPL
NM_025152.3 intron
NM_025152.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.444
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 14-31562039-C-T is Benign according to our data. Variant chr14-31562039-C-T is described in ClinVar as [Benign]. Clinvar id is 1232898.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0519 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUBPL | NM_025152.3 | c.109-29C>T | intron_variant | ENST00000281081.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUBPL | ENST00000281081.12 | c.109-29C>T | intron_variant | 1 | NM_025152.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0347 AC: 5282AN: 152068Hom.: 124 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
5282
AN:
152068
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0356 AC: 5549AN: 155840Hom.: 156 AF XY: 0.0354 AC XY: 2939AN XY: 82950
GnomAD3 exomes
AF:
AC:
5549
AN:
155840
Hom.:
AF XY:
AC XY:
2939
AN XY:
82950
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0483 AC: 67412AN: 1397112Hom.: 1909 Cov.: 30 AF XY: 0.0475 AC XY: 32760AN XY: 689386
GnomAD4 exome
AF:
AC:
67412
AN:
1397112
Hom.:
Cov.:
30
AF XY:
AC XY:
32760
AN XY:
689386
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0347 AC: 5281AN: 152186Hom.: 124 Cov.: 32 AF XY: 0.0325 AC XY: 2414AN XY: 74380
GnomAD4 genome
?
AF:
AC:
5281
AN:
152186
Hom.:
Cov.:
32
AF XY:
AC XY:
2414
AN XY:
74380
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
25
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 07, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at