chr22:41926712:G>C Detail (hg38) (TNFRSF13C, LOC130067574)

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Information

Genome

Assembly	Position
hg19	chr22:42,322,716-42,322,716 View the variant detail on this assembly version.
hg38	chr22:41,926,712-41,926,712

Type	Transcript	Protein
RefSeq	NM_052945.3:c.62C>G	NP_443177.1:p.Pro21Arg
Ensemble	ENST00000291232.5:c.62C>G	ENST00000291232.5:p.Pro21Arg

Summary

Clinical Significance	Conflicting classifications of pathogenicity
Review star
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Links

Type	Database	ID	Link
Gene	MIM	606269	OMIM
	HGNC	17755	HGNC
	Ensembl	ENSG00000159958	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv66042576	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign Likely benign	2024-02-01	criteria provided, multiple submitters, no conflicts	Immunodeficiency, common variable, 4	germline	Detail
Conflicting interpretations of pathogenicity	2020-07-22	criteria provided, conflicting interpretations	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.010	Septicemia	Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated wit...	BeFree	25454804	Detail
0.244	Sepsis	Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated wit...	BeFree	25454804	Detail
<0.001	Sepsis	Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated wit...	BeFree	25454804	Detail
<0.001	Septicemia	Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated wit...	BeFree	25454804	Detail

Annotation

Descrption	Source	Links
NM_052945.4(TNFRSF13C):c.62C>G (p.Pro21Arg) AND Immunodeficiency, common variable, 4	ClinVar	Detail
NM_052945.4(TNFRSF13C):c.62C>G (p.Pro21Arg) AND not provided	ClinVar	Detail
Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated with a lower risk of IC...	DisGeNET	Detail
Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated with a lower risk of IC...	DisGeNET	Detail
Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated with a lower risk of IC...	DisGeNET	Detail
Interestingly, TLR4-D299G, TLR4-T399I and BAFFR-P21R carriage was associated with a lower risk of IC...	DisGeNET	Detail

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs77874543 dbSNP
Genome: hg38
Position: chr22:41,926,712-41,926,712
Variant Type: snv
Reference Allele: G
Alternative Allele: C
Filtering Status (HGVD): PASS
Filtering Status (HGVD): LowQual
# of samples (HGVD): 1055
Mean of sample read depth (HGVD): 33.48
Standard deviation of sample read depth (HGVD): 13.58
Number of reference allele (HGVD): 2028
Number of alternative allele (HGVD): 82
Allele Frequency (HGVD): 0.03886255924170616
Gene Symbol (HGVD): TNFRSF13C
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)): rs77874543
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0476
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 798
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16752
East Asian Chromosome Counts (ExAC): 104
East Asian Allele Counts (ExAC): 2
East Asian Heterozygous Counts (ExAC): 2
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 0.019230769230769232
Chromosome Counts in All Race (ExAC): 7938
Allele Counts in All Race (ExAC): 540
Heterozygous Counts in All Race (ExAC): 492
Homozygous Counts in All Race (ExAC): 24
Allele Frequency in All Race (ExAC): 0.06802721088435375

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