chr7:41978737:G>A Detail (hg38) (GLI3)

Information

Genome

Assembly Position
hg19 chr7:42,018,336-42,018,336 View the variant detail on this assembly version.
hg38 chr7:41,978,737-41,978,737

HGVS

Type Transcript Protein
RefSeq NM_000168.5:c.1509C>T NP_000159.3:p.Asn503=
Ensemble ENST00000677288.1:c.1335C>T ENST00000677288.1:p.Asn445=
ENST00000395925.8:c.1509C>T ENST00000395925.8:p.Asn503=
Summary

MGeND

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

Frequency

JP HGVD:0.005
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.003

Prediction

ClinVar

Clinical Significance 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 tgv29044144 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 criteria provided, single submitter not specified germline Detail
Benign 2018-01-12 criteria provided, single submitter Pallister-Hall syndrome germline Detail
Benign 2018-01-12 criteria provided, single submitter Greig cephalopolysyndactyly syndrome germline Detail
Benign 2018-01-12 criteria provided, single submitter polydactyly germline Detail
Benign 2024-01-31 criteria provided, single submitter Pallister-Hall syndrome,Greig cephalopolysyndactyly syndrome germline Detail
Benign 2024-01-31 criteria provided, single submitter Pallister-Hall syndrome,Greig cephalopolysyndactyly syndrome germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000168.6(GLI3):c.1509C>T (p.Asn503=) AND not specified ClinVar Detail
NM_000168.6(GLI3):c.1509C>T (p.Asn503=) AND Pallister-Hall syndrome ClinVar Detail
NM_000168.6(GLI3):c.1509C>T (p.Asn503=) AND Greig cephalopolysyndactyly syndrome ClinVar Detail
NM_000168.6(GLI3):c.1509C>T (p.Asn503=) AND Polydactyly ClinVar Detail
NM_000168.6(GLI3):c.1509C>T (p.Asn503=) AND multiple conditions ClinVar Detail
NM_000168.6(GLI3):c.1509C>T (p.Asn503=) AND multiple conditions ClinVar Detail
NM_000168.6(GLI3):c.1509C>T (p.Asn503=) 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
rs34020684 dbSNP
Genome
hg38
Position
chr7:41,978,737-41,978,737
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1202
Mean of sample read depth (HGVD)
41.15
Standard deviation of sample read depth (HGVD)
23.29
Number of reference allele (HGVD)
2392
Number of alternative allele (HGVD)
12
Allele Frequency (HGVD)
0.004991680532445923
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))
rs34020684
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0025
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
42
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8638
East Asian Allele Counts (ExAC)
30
East Asian Heterozygous Counts (ExAC)
30
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.003473026163463765
Chromosome Counts in All Race (ExAC)
121288
Allele Counts in All Race (ExAC)
4458
Heterozygous Counts in All Race (ExAC)
4272
Homozygous Counts in All Race (ExAC)
93
Allele Frequency in All Race (ExAC)
0.03675549106259481
Genome browser