chr1:10326309:C>T Detail (hg38) (KIF1B, LOC126805614)

Information

Genome

Assembly Position
hg19 chr1:10,386,367-10,386,367 View the variant detail on this assembly version.
hg38 chr1:10,326,309-10,326,309

HGVS

Type Transcript Protein
RefSeq NM_015074.3:c.2736C>T NP_055889.2:p.Asp912=
Ensemble ENST00000263934.10:c.2736C>T ENST00000263934.10:p.Asp912=
ENST00000377081.5:c.2874C>T ENST00000377081.5:p.Asp958=
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.021
ToMMo:0.020
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.019

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605995 OMIM
HGNC 16636 HGNC
Ensembl ENSG00000054523 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv330184 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-01-12 criteria provided, single submitter neuroblastoma germline Detail
Benign 2024-01-06 criteria provided, single submitter Charcot-Marie-Tooth disease type 2 germline Detail
Likely benign criteria provided, single submitter Charcot-Marie-Tooth disease germline Detail
Likely benign 2020-09-03 criteria provided, single submitter not specified germline Detail
Benign 2020-07-02 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_001365951.3(KIF1B):c.2874C>T (p.Asp958=) AND Neuroblastoma ClinVar Detail
NM_001365951.3(KIF1B):c.2874C>T (p.Asp958=) AND Charcot-Marie-Tooth disease type 2 ClinVar Detail
NM_001365951.3(KIF1B):c.2874C>T (p.Asp958=) AND Charcot-Marie-Tooth disease ClinVar Detail
NM_001365951.3(KIF1B):c.2874C>T (p.Asp958=) AND not specified ClinVar Detail
NM_001365951.3(KIF1B):c.2874C>T (p.Asp958=) AND not provided ClinVar Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs150831576 dbSNP
Genome
hg38
Position
chr1:10,326,309-10,326,309
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
109.85
Standard deviation of sample read depth (HGVD)
54.39
Number of reference allele (HGVD)
2368
Number of alternative allele (HGVD)
52
Allele Frequency (HGVD)
0.021487603305785124
Gene Symbol (HGVD)
KIF1B
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs150831576
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0196
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
329
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
164
East Asian Heterozygous Counts (ExAC)
158
East Asian Homozygous Counts (ExAC)
3
East Asian Allele Frequency (ExAC)
0.018963922294172063
Chromosome Counts in All Race (ExAC)
121384
Allele Counts in All Race (ExAC)
206
Heterozygous Counts in All Race (ExAC)
200
Homozygous Counts in All Race (ExAC)
3
Allele Frequency in All Race (ExAC)
0.0016970935213866736
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