rs16926021
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015634.4(KIFBP):c.1023G>A(p.Gln341=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,613,426 control chromosomes in the GnomAD database, including 1,459 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.055 ( 761 hom., cov: 32)
Exomes 𝑓: 0.0056 ( 698 hom. )
Consequence
KIFBP
NM_015634.4 synonymous
NM_015634.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.113
Genes affected
KIFBP (HGNC:23419): (kinesin family binding protein) This gene encodes a kinesin family member 1 binding protein that is characterized by two tetratrico peptide repeats. The encoded protein localizes to the mitochondria and may be involved in regulating transport of the mitochondria. Mutations in this gene are associated with Goldberg-Shprintzen megacolon syndrome. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 10-69015573-G-A is Benign according to our data. Variant chr10-69015573-G-A is described in ClinVar as [Benign]. Clinvar id is 158692.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-69015573-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=0.113 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIFBP | NM_015634.4 | c.1023G>A | p.Gln341= | synonymous_variant | 7/7 | ENST00000361983.7 | |
KIFBP | XM_017016067.2 | c.225G>A | p.Gln75= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIFBP | ENST00000361983.7 | c.1023G>A | p.Gln341= | synonymous_variant | 7/7 | 1 | NM_015634.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0547 AC: 8310AN: 151916Hom.: 753 Cov.: 32
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GnomAD3 exomes AF: 0.0140 AC: 3519AN: 250868Hom.: 292 AF XY: 0.0106 AC XY: 1436AN XY: 135686
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GnomAD4 exome AF: 0.00562 AC: 8217AN: 1461392Hom.: 698 Cov.: 32 AF XY: 0.00487 AC XY: 3540AN XY: 727012
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GnomAD4 genome ? AF: 0.0549 AC: 8350AN: 152034Hom.: 761 Cov.: 32 AF XY: 0.0526 AC XY: 3909AN XY: 74324
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Goldberg-Shprintzen syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
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