chr9:95447312:G>A Detail (hg38) (PTCH1)

Information

Genome

Assembly Position
hg19 chr9:98,209,594-98,209,594 View the variant detail on this assembly version.
hg38 chr9:95,447,312-95,447,312

HGVS

Type Transcript Protein
RefSeq NM_000264.3:c.3944C>T NP_000255.2:p.Pro1315Leu
NM_001083606.1:c.3491C>T NP_001077075.1:p.Pro1164Leu
NM_001083602.1:c.3941C>T NP_001077071.1:p.Pro1314Leu
Summary

MGeND

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

Frequency

JP HGVD:0.604
ToMMo:0.614
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.567

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601309 OMIM
HGNC 9585 HGNC
Ensembl ENSG00000185920 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv36904420 TogoVar
COSMIC COSM1638394 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 2023-11-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2016-03-28 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Gorlin syndrome germline Detail
Benign 2021-10-25 criteria provided, multiple submitters, no conflicts holoprosencephaly 7 germline Detail
Benign 2014-12-01 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000264.5(PTCH1):c.3944C>T (p.Pro1315Leu) AND not provided ClinVar Detail
NM_000264.5(PTCH1):c.3944C>T (p.Pro1315Leu) AND not specified ClinVar Detail
NM_000264.5(PTCH1):c.3944C>T (p.Pro1315Leu) AND Gorlin syndrome ClinVar Detail
NM_000264.5(PTCH1):c.3944C>T (p.Pro1315Leu) AND Holoprosencephaly 7 ClinVar Detail
NM_000264.5(PTCH1):c.3944C>T (p.Pro1315Leu) AND Hereditary cancer-predisposing syndrome 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
rs357564 dbSNP
Genome
hg38
Position
chr9:95,447,312-95,447,312
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1166
Mean of sample read depth (HGVD)
52.67
Standard deviation of sample read depth (HGVD)
24.52
Number of reference allele (HGVD)
923
Number of alternative allele (HGVD)
1406
Allele Frequency (HGVD)
0.6036925719192786
Gene Symbol (HGVD)
PTCH1
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))
rs357564
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6143
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10294
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8498
East Asian Allele Counts (ExAC)
4816
East Asian Heterozygous Counts (ExAC)
2056
East Asian Homozygous Counts (ExAC)
1380
East Asian Allele Frequency (ExAC)
0.5667215815485996
Chromosome Counts in All Race (ExAC)
116034
Allele Counts in All Race (ExAC)
44727
Heterozygous Counts in All Race (ExAC)
26475
Homozygous Counts in All Race (ExAC)
9126
Allele Frequency in All Race (ExAC)
0.38546460520192355
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