chr11:71807826:C>T Detail (hg19) (LAMTOR1, LRTOMT, LRRC51)

Information

Genome

Assembly Position
hg19 chr11:71,807,826-71,807,826
hg38 chr11:72,096,780-72,096,780 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000545249.5:c.393+1509G>A
ENST00000535107.5:c.266+2001G>A
Type Transcript Protein
RefSeq NM_001145307.4:c.*18C>T
NM_001271471.2:c.*1260C>T
NM_001318803.1:c.*1260C>T
Type Transcript Protein
RefSeq NM_001145308.4:c.34+1684C>T
NM_001145309.3:c.34+1684C>T
Ensemble ENST00000643715.1:c.437+1684C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.010
ToMMo:0.011
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.025

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613510 OMIM
HGNC 26068 HGNC
Ensembl ENSG00000149357 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv43130373 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM
HGNC 55526 HGNC
Ensembl ENSG00000184154 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv43130373 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 612414 OMIM
HGNC 25033 HGNC
Ensembl ENSG00000284922 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv43130373 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Likely benign 2019-06-09 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_145309.6(LRRC51):c.*1260C>T 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
rs79601663 dbSNP
Genome
hg19
Position
chr11:71,807,826-71,807,826
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
836
Mean of sample read depth (HGVD)
85.37
Standard deviation of sample read depth (HGVD)
40.67
Number of reference allele (HGVD)
1656
Number of alternative allele (HGVD)
16
Allele Frequency (HGVD)
0.009569377990430622
Gene Symbol (HGVD)
LRTOMT
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))
rs79601663
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0106
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
178
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
550
East Asian Allele Counts (ExAC)
14
East Asian Heterozygous Counts (ExAC)
14
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.025454545454545455
Chromosome Counts in All Race (ExAC)
15512
Allele Counts in All Race (ExAC)
15
Heterozygous Counts in All Race (ExAC)
15
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
9.669932955131511E-4
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