NM_015074.3(KIF1B):c.1977+6360G>T AND not provided

Clinical significance:Likely benign

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV001357609.3

Allele description [Variation Report for NM_015074.3(KIF1B):c.1977+6360G>T]

NM_015074.3(KIF1B):c.1977+6360G>T

Gene:
KIF1B:kinesin family member 1B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.22
Genomic location:
Preferred name:
NM_015074.3(KIF1B):c.1977+6360G>T
HGVS:
  • NC_000001.11:g.10303606G>T
  • NG_008069.1:g.97901G>T
  • NM_001365951.2:c.2115+6360G>T
  • NM_001365952.1:c.2115+6360G>T
  • NM_001365953.1:c.2421G>T
  • NM_015074.3:c.1977+6360G>T
  • NM_183416.4:c.2421G>T
  • NP_001352882.1:p.Met807Ile
  • NP_904325.2:p.Met807Ile
  • LRG_252t1:c.1977+6360G>T
  • LRG_252:g.97901G>T
  • NC_000001.10:g.10363664G>T
  • NM_183416.3:c.2421G>T
Protein change:
M807I
Links:
dbSNP: rs41274458
NCBI 1000 Genomes Browser:
rs41274458
Molecular consequence:
  • NM_001365951.2:c.2115+6360G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001365952.1:c.2115+6360G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_015074.3:c.1977+6360G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001365953.1:c.2421G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_183416.4:c.2421G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001553125Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedLikely benignunknownclinical testing

SCV001798697Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensusno assertion criteria providedLikely benigngermlineclinical testing

SCV001929450Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus

See additional submitters

no assertion criteria providedLikely benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001553125.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001798697.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001929450.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 24, 2021

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