ClinVar Miner

Submissions for variant NM_001365951.3(KIF1B):c.2115+6360G>T

gnomAD frequency: 0.01961  dbSNP: rs41274458
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia RCV000202848 SCV000258273 benign not specified 2015-02-13 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001357609 SCV001159541 benign not provided 2023-11-22 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001357609 SCV001553125 likely benign not provided no assertion criteria provided clinical testing The KIF1B p.Met807Ile variant was identified in dbSNP (ID: rs41274458) and ClinVar (classified as benign by the Division of Genomic Diagnostics, The Children's Hospital of Philadelphia) but was not identified in Cosmic or LOVD 3.0. The variant was also identified in control databases in 5217 of 282018 chromosomes (87 homozygous) at a frequency of 0.018499 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: European (Finnish) in 1052 of 25118 chromosomes (freq: 0.04188), European (non-Finnish) in 3406 of 128482 chromosomes (freq: 0.02651), Other in 153 of 7206 chromosomes (freq: 0.02123), Latino in 346 of 35412 chromosomes (freq: 0.009771), Ashkenazi Jewish in 70 of 10320 chromosomes (freq: 0.006783), African in 102 of 24938 chromosomes (freq: 0.00409), South Asian in 87 of 30608 chromosomes (freq: 0.002842) and East Asian in 1 of 19934 chromosomes (freq: 0.00005). This variant was previously reported somatically in neuroblastoma tumors (Chen_2014_PMID: 24469107). 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.Met807 residue is not conserved in mammals and 5 of 5 computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein. 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.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001357609 SCV001798697 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000202848 SCV001919203 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001357609 SCV001929450 likely benign not provided no assertion criteria provided clinical testing

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