chr14-31561965-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_025152.3(NUBPL):c.109-103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00131 in 1,129,496 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0059 ( 8 hom., cov: 32)
Exomes 𝑓: 0.00060 ( 3 hom. )
Consequence
NUBPL
NM_025152.3 intron
NM_025152.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.136
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=-0.24).
BP6
?
Variant 14-31561965-G-A is Benign according to our data. Variant chr14-31561965-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1198691.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0059 (898/152314) while in subpopulation AFR AF= 0.0202 (839/41556). AF 95% confidence interval is 0.0191. There are 8 homozygotes in gnomad4. There are 412 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUBPL | NM_025152.3 | c.109-103G>A | intron_variant | ENST00000281081.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUBPL | ENST00000281081.12 | c.109-103G>A | intron_variant | 1 | NM_025152.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00591 AC: 899AN: 152196Hom.: 8 Cov.: 32
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GnomAD4 exome AF: 0.000599 AC: 585AN: 977182Hom.: 3 AF XY: 0.000523 AC XY: 261AN XY: 498692
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GnomAD4 genome ? AF: 0.00590 AC: 898AN: 152314Hom.: 8 Cov.: 32 AF XY: 0.00553 AC XY: 412AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 30, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at