chr7:42048700:G>A Detail (hg38) (GLI3)

Information

Genome

Assembly Position
hg19 chr7:42,088,299-42,088,299 View the variant detail on this assembly version.
hg38 chr7:42,048,700-42,048,700

HGVS

Type Transcript Protein
RefSeq NM_000168.5:c.474-4C>T
Ensemble ENST00000395925.8:c.474-4C>T
ENST00000479210.1:c.297-4C>T
Summary

MGeND

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

Frequency

JP HGVD:0.019
ToMMo:0.021
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.011

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 165240 OMIM
HGNC 4319 HGNC
Ensembl ENSG00000106571 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv29045826 TogoVar
COSMIC COSM3685170 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
Likely benign 2017-04-27 criteria provided, single submitter Greig cephalopolysyndactyly syndrome germline Detail
Likely benign 2017-04-27 criteria provided, single submitter polydactyly germline Detail
Likely benign 2017-04-27 criteria provided, single submitter Pallister-Hall syndrome germline Detail
Benign 2023-09-04 criteria provided, single submitter Pallister-Hall syndrome,Greig cephalopolysyndactyly syndrome germline Detail
Benign 2023-09-04 criteria provided, single submitter Pallister-Hall syndrome,Greig cephalopolysyndactyly syndrome germline Detail
Likely benign 2020-10-06 criteria provided, single submitter not provided germline Detail
Likely benign 2021-08-16 criteria provided, single submitter Greig cephalopolysyndactyly syndrome,Polysyndactyly 4,Pallister-Hall syndrome,Polydactyly, postaxial, type A1 unknown Detail
Likely benign 2021-08-16 criteria provided, single submitter Greig cephalopolysyndactyly syndrome,Polysyndactyly 4,Pallister-Hall syndrome,Polydactyly, postaxial, type A1 unknown Detail
Likely benign 2021-08-16 criteria provided, single submitter Greig cephalopolysyndactyly syndrome,Polysyndactyly 4,Pallister-Hall syndrome,Polydactyly, postaxial, type A1 unknown Detail
Likely benign 2021-08-16 criteria provided, single submitter Greig cephalopolysyndactyly syndrome,Polysyndactyly 4,Pallister-Hall syndrome,Polydactyly, postaxial, type A1 unknown Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000168.6(GLI3):c.474-4C>T AND Greig cephalopolysyndactyly syndrome ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND Polydactyly ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND Pallister-Hall syndrome ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND multiple conditions ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND multiple conditions ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND not provided ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND multiple conditions ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND multiple conditions ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND multiple conditions ClinVar Detail
NM_000168.6(GLI3):c.474-4C>T AND multiple conditions ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs74536326 dbSNP
Genome
hg38
Position
chr7:42,048,700-42,048,700
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1167
Mean of sample read depth (HGVD)
33.90
Standard deviation of sample read depth (HGVD)
17.09
Number of reference allele (HGVD)
2289
Number of alternative allele (HGVD)
45
Allele Frequency (HGVD)
0.019280205655526992
Gene Symbol (HGVD)
GLI3
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))
rs74536326
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0208
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
349
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
6724
East Asian Allele Counts (ExAC)
74
East Asian Heterozygous Counts (ExAC)
74
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.011005353955978583
Chromosome Counts in All Race (ExAC)
98632
Allele Counts in All Race (ExAC)
118
Heterozygous Counts in All Race (ExAC)
118
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
0.0011963662908589503
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