chr11:36575763:A>G Detail (hg38) (RAG1)

Information

Genome

Assembly Position
hg19 chr11:36,597,313-36,597,313 View the variant detail on this assembly version.
hg38 chr11:36,575,763-36,575,763

HGVS

Type Transcript Protein
RefSeq NM_000448.2:c.2459A>G NP_000439.1:p.Lys820Arg
Ensemble ENST00000299440.6:c.2459A>G ENST00000299440.6:p.Lys820Arg
ENST00000697713.1:c.2459A>G ENST00000697713.1:p.Lys820Arg
Summary

MGeND

Clinical significance Likely pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.573
ToMMo:0.600
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.599

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 179615 OMIM
HGNC 9831 HGNC
Ensembl ENSG00000166349 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv42206147 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely pathogenic other germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-24 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-11-07 criteria provided, multiple submitters, no conflicts severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, Nk cell-positive germline Detail
Benign 2021-11-07 criteria provided, multiple submitters, no conflicts Histiocytic medullary reticulosis germline Detail
Benign 2024-02-01 criteria provided, single submitter severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, Nk cell-positive,Combined immunodeficiency with skin granulomas germline Detail
Benign 2024-02-01 criteria provided, single submitter severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, Nk cell-positive,Combined immunodeficiency with skin granulomas germline Detail
Benign 2015-03-03 criteria provided, single submitter not provided germline Detail
Benign 2021-11-07 criteria provided, single submitter Combined immunodeficiency with skin granulomas germline Detail
Benign criteria provided, single submitter Immunodeficiency 104 germline Detail
Benign 2024-01-23 reviewed by expert panel recombinase activating gene 1 deficiency germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 Lymphoma, Follicular We have genotyped polymorphisms in the RAG1 (K820R), LIG4 (T9I), BRCA2 (N372H), ... BeFree 21476145 Detail
0.003 Lymphoma, Follicular We have genotyped polymorphisms in the RAG1 (K820R), LIG4 (T9I), BRCA2 (N372H), ... BeFree 21476145 Detail
0.003 Lymphoma, Follicular We have genotyped polymorphisms in the RAG1 (K820R), LIG4 (T9I), BRCA2 (N372H), ... BeFree 21476145 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND not specified ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND Severe combined immunodeficiency, autosomal recessive,... ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND Histiocytic medullary reticulosis ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND multiple conditions ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND multiple conditions ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND not provided ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND Combined immunodeficiency with skin granulomas ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND Immunodeficiency 104 ClinVar Detail
NM_000448.3(RAG1):c.2459A>G (p.Lys820Arg) AND Recombinase activating gene 1 deficiency ClinVar Detail
We have genotyped polymorphisms in the RAG1 (K820R), LIG4 (T9I), BRCA2 (N372H), and WRN (V114I) gene... DisGeNET Detail
We have genotyped polymorphisms in the RAG1 (K820R), LIG4 (T9I), BRCA2 (N372H), and WRN (V114I) gene... DisGeNET Detail
We have genotyped polymorphisms in the RAG1 (K820R), LIG4 (T9I), BRCA2 (N372H), and WRN (V114I) gene... DisGeNET 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
rs2227973 dbSNP
Genome
hg38
Position
chr11:36,575,763-36,575,763
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1128
Mean of sample read depth (HGVD)
61.02
Standard deviation of sample read depth (HGVD)
34.61
Number of reference allele (HGVD)
962
Number of alternative allele (HGVD)
1292
Allele Frequency (HGVD)
0.5732031943212067
Gene Symbol (HGVD)
RAG1
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))
rs2227973
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6005
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10064
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8630
East Asian Allele Counts (ExAC)
5173
East Asian Heterozygous Counts (ExAC)
2085
East Asian Homozygous Counts (ExAC)
1544
East Asian Allele Frequency (ExAC)
0.5994206257242178
Chromosome Counts in All Race (ExAC)
121170
Allele Counts in All Race (ExAC)
22610
Heterozygous Counts in All Race (ExAC)
15728
Homozygous Counts in All Race (ExAC)
3441
Allele Frequency in All Race (ExAC)
0.18659734257654534
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