rs2280231
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018095.6(KBTBD4):c.19+47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,550,998 control chromosomes in the GnomAD database, including 55,810 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.20 ( 3863 hom., cov: 31)
Exomes 𝑓: 0.27 ( 51947 hom. )
Consequence
KBTBD4
NM_018095.6 intron
NM_018095.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0560
Genes affected
KBTBD4 (HGNC:23761): (kelch repeat and BTB domain containing 4)
NDUFS3 (HGNC:7710): (NADH:ubiquinone oxidoreductase core subunit S3) This gene encodes one of the iron-sulfur protein (IP) components of mitochondrial NADH:ubiquinone oxidoreductase (complex I). Mutations in this gene are associated with Leigh syndrome resulting from mitochondrial complex I deficiency.[provided by RefSeq, Apr 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 11-47578886-C-T is Benign according to our data. Variant chr11-47578886-C-T is described in ClinVar as [Benign]. Clinvar id is 1239179.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KBTBD4 | NM_018095.6 | c.19+47G>A | intron_variant | ENST00000430070.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KBTBD4 | ENST00000430070.7 | c.19+47G>A | intron_variant | 1 | NM_018095.6 |
Frequencies
GnomAD3 genomes ? AF: 0.201 AC: 30437AN: 151786Hom.: 3863 Cov.: 31
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GnomAD3 exomes AF: 0.241 AC: 37435AN: 155152Hom.: 5108 AF XY: 0.250 AC XY: 20569AN XY: 82290
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GnomAD4 exome AF: 0.267 AC: 373575AN: 1399090Hom.: 51947 Cov.: 40 AF XY: 0.268 AC XY: 185113AN XY: 690046
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GnomAD4 genome ? AF: 0.200 AC: 30423AN: 151908Hom.: 3863 Cov.: 31 AF XY: 0.196 AC XY: 14580AN XY: 74224
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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 | Jun 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at