chr7:142460313:T>C Detail (hg19) (PRSS1, TRB)

Information

Genome

Assembly Position
hg19 chr7:142,460,313-142,460,313
hg38 chr7:142,752,462-142,752,462 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000311737.12:c.486T>C ENST00000311737.12:p.Asp162=
ENST00000486171.5:c.528T>C ENST00000486171.5:p.Asp176=
Summary

MGeND

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

Frequency

JP HGVD:0.187
ToMMo:0.262
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.202

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 276000 OMIM
HGNC 9475 HGNC
Ensembl ENSG00000204983 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv31280442 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 2024-02-01 criteria provided, multiple submitters, no conflicts Hereditary pancreatitis germline Detail
Benign Likely benign 2021-04-21 criteria provided, multiple submitters, no conflicts not specified germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_002769.5(PRSS1):c.486T>C (p.Asp162=) AND Hereditary pancreatitis ClinVar Detail
NM_002769.5(PRSS1):c.486T>C (p.Asp162=) AND not specified 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
rs6666 dbSNP
Genome
hg19
Position
chr7:142,460,313-142,460,313
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
# of samples (HGVD)
1030
Mean of sample read depth (HGVD)
38.72
Standard deviation of sample read depth (HGVD)
92.20
Number of reference allele (HGVD)
1675
Number of alternative allele (HGVD)
385
Allele Frequency (HGVD)
0.18689320388349515
Gene Symbol (HGVD)
PRSS1
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))
rs6666
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2625
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4399
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
1750
East Asian Heterozygous Counts (ExAC)
1750
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.2022186272244049
Chromosome Counts in All Race (ExAC)
121396
Allele Counts in All Race (ExAC)
44826
Heterozygous Counts in All Race (ExAC)
44826
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
0.36925434116445355
Genome browser