chr1:247424229:A>G Detail (hg38) (NLRP3)

Information

Genome

Assembly Position
hg19 chr1:247,587,531-247,587,531 View the variant detail on this assembly version.
hg38 chr1:247,424,229-247,424,229

HGVS

Type Transcript Protein
RefSeq NM_001127462.2:c.780A>G NP_001120934.1:p.Arg260=
NM_001243133.1:c.780A>G NP_001230062.1:p.Arg260=
NM_004895.4:c.780A>G NP_004886.3:p.Arg260=
Summary

MGeND

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

Frequency

JP HGVD:0.999
ToMMo:1.000
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.999

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606416 OMIM
HGNC 16400 HGNC
Ensembl ENSG00000162711 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv5541979 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 2023-11-12 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, single submitter Cryopyrin associated periodic syndrome germline Detail
Benign 2021-09-05 criteria provided, single submitter familial cold autoinflammatory syndrome 1 germline Detail
Benign 2021-09-05 criteria provided, single submitter Familial amyloid nephropathy with urticaria AND deafness germline Detail
Benign 2021-09-05 criteria provided, single submitter Chronic infantile neurological, cutaneous and articular syndrome germline Detail
Benign 2021-09-05 criteria provided, single submitter Keratitis fugax hereditaria germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_001243133.2(NLRP3):c.780A>G (p.Arg260=) AND not specified ClinVar Detail
NM_001243133.2(NLRP3):c.780A>G (p.Arg260=) AND Cryopyrin associated periodic syndrome ClinVar Detail
NM_001243133.2(NLRP3):c.780A>G (p.Arg260=) AND Familial cold autoinflammatory syndrome 1 ClinVar Detail
NM_001243133.2(NLRP3):c.780A>G (p.Arg260=) AND Familial amyloid nephropathy with urticaria AND deafn... ClinVar Detail
NM_001243133.2(NLRP3):c.780A>G (p.Arg260=) AND Chronic infantile neurological, cutaneous and articul... ClinVar Detail
NM_001243133.2(NLRP3):c.780A>G (p.Arg260=) AND Keratitis fugax hereditaria ClinVar Detail
NM_001243133.2(NLRP3):c.780A>G (p.Arg260=) 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
rs4925543 dbSNP
Genome
hg38
Position
chr1:247,424,229-247,424,229
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
171.79
Standard deviation of sample read depth (HGVD)
77.02
Number of reference allele (HGVD)
2
Number of alternative allele (HGVD)
2412
Allele Frequency (HGVD)
0.9991714995857498
Gene Symbol (HGVD)
NLRP3
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))
rs4925543
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
8642
East Asian Heterozygous Counts (ExAC)
12
East Asian Homozygous Counts (ExAC)
4315
East Asian Allele Frequency (ExAC)
0.9986133579847469
Chromosome Counts in All Race (ExAC)
121398
Allele Counts in All Race (ExAC)
114429
Heterozygous Counts in All Race (ExAC)
6323
Homozygous Counts in All Race (ExAC)
54053
Allele Frequency in All Race (ExAC)
0.9425937824346365
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