ClinVar Miner

Submissions for variant NM_001365951.3(KIF1B):c.2115+6956A>G

gnomAD frequency: 0.00525  dbSNP: rs148481786
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000281337 SCV000335078 benign not specified 2015-09-28 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000423645 SCV000511663 likely benign not provided 2017-01-04 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000423645 SCV001472878 benign not provided 2023-11-22 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000423645 SCV004042414 benign not provided 2024-04-01 criteria provided, single submitter clinical testing KIF1B: PP2, BP4, BS1, BS2
PreventionGenetics, part of Exact Sciences RCV003920059 SCV004735870 benign KIF1B-related disorder 2019-04-17 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Center of Medical Genetics and Primary Health Care RCV001270154 SCV001450447 likely benign Malignant tumor of breast no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000423645 SCV001550051 likely benign not provided no assertion criteria provided clinical testing The KIF1B p.Glu1006Gly variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs148481786) and ClinVar (classified as benign by EGL Genetics and likely benign by Children's Mercy Hospital) The variant was identified in control databases in 1644 of 282350 chromosomes (14 homozygous) at a frequency of 0.005823 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Ashkenazi Jewish in 290 of 10356 chromosomes (freq: 0.028), European (Finnish) in 249 of 25120 chromosomes (freq: 0.009912), Other in 67 of 7192 chromosomes (freq: 0.009316), European (non-Finnish) in 859 of 128920 chromosomes (freq: 0.006663), Latino in 89 of 35424 chromosomes (freq: 0.002512), South Asian in 71 of 30614 chromosomes (freq: 0.002319) and African in 19 of 24776 chromosomes (freq: 0.000767), while the variant was not observed in the East Asian population. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Glu1006 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.
Clinical Genetics, Academic Medical Center RCV000281337 SCV001925285 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000423645 SCV001929787 likely benign not provided no assertion criteria provided clinical testing

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