rs104894649

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS1

The NM_012452.3(TNFRSF13B):​c.605G>A​(p.Arg202His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000969 in 1,613,764 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00073 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00099 ( 1 hom. )

Consequence

TNFRSF13B
NM_012452.3 missense

Scores

3
16

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:4B:4

Conservation

PhyloP100: 1.74
Variant links:
Genes affected
TNFRSF13B (HGNC:18153): (TNF receptor superfamily member 13B) The protein encoded by this gene is a lymphocyte-specific member of the tumor necrosis factor (TNF) receptor superfamily. It interacts with calcium-modulator and cyclophilin ligand (CAML). The protein induces activation of the transcription factors NFAT, AP1, and NF-kappa-B and plays a crucial role in humoral immunity by interacting with a TNF ligand. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.23804653).
BP6
Variant 17-16940352-C-T is Benign according to our data. Variant chr17-16940352-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 5304.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=4, Benign=1, Likely_benign=3}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000729 (111/152282) while in subpopulation NFE AF= 0.00119 (81/68022). AF 95% confidence interval is 0.000981. There are 0 homozygotes in gnomad4. There are 54 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TNFRSF13BNM_012452.3 linkc.605G>A p.Arg202His missense_variant Exon 4 of 5 ENST00000261652.7 NP_036584.1 O14836-1Q4ACX1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNFRSF13BENST00000261652.7 linkc.605G>A p.Arg202His missense_variant Exon 4 of 5 1 NM_012452.3 ENSP00000261652.2 O14836-1

Frequencies

GnomAD3 genomes
AF:
0.000729
AC:
111
AN:
152164
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000217
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00119
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000796
AC:
199
AN:
249890
Hom.:
0
AF XY:
0.000784
AC XY:
106
AN XY:
135180
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.000463
Gnomad ASJ exome
AF:
0.00318
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.0000924
Gnomad NFE exome
AF:
0.00123
Gnomad OTH exome
AF:
0.000489
GnomAD4 exome
AF:
0.000994
AC:
1452
AN:
1461482
Hom.:
1
Cov.:
31
AF XY:
0.000968
AC XY:
704
AN XY:
727038
show subpopulations
Gnomad4 AFR exome
AF:
0.000120
Gnomad4 AMR exome
AF:
0.000581
Gnomad4 ASJ exome
AF:
0.00253
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000812
Gnomad4 FIN exome
AF:
0.0000749
Gnomad4 NFE exome
AF:
0.00116
Gnomad4 OTH exome
AF:
0.000878
GnomAD4 genome
AF:
0.000729
AC:
111
AN:
152282
Hom.:
0
Cov.:
32
AF XY:
0.000725
AC XY:
54
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.000217
Gnomad4 AMR
AF:
0.000719
Gnomad4 ASJ
AF:
0.00144
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00119
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00131
Hom.:
0
Bravo
AF:
0.000846
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00104
AC:
4
ESP6500AA
AF:
0.000454
AC:
2
ESP6500EA
AF:
0.000814
AC:
7
ExAC
AF:
0.000766
AC:
93
EpiCase
AF:
0.00104
EpiControl
AF:
0.00184

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:4Benign:4
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:4
Sep 03, 2021
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The TNFRSF13B c.605G>A; p.Arg202His variant (rs104894649) is reported in literature in six individuals affected with common variable immune deficiency (Janzi 2012, Pan-Hammarström 2007, Salzer 2005) and two individuals with IgAD (Pan-Hammarström 2007). This variant was more frequently observed in control individuals compared to CVID cohort, though an enrichment was observed in IgAD cohort compared to controls with an odds ratio of 5.91 (1.94~18.07, 95% CI) (Pan-Hammarström 2007). Data obtained from a single IgAD patient suggested that this variant does not alter IgA levels (Janzi 2012). Functional analyses of the variant protein by luciferase reporter assay showed no impact on downstream signaling pathway components (He 2010). This variant is also reported in ClinVar (Variation ID: 5304). This variant is found in the non-Finnish European population with an allele frequency of 0.12% (156/127656 alleles) in the Genome Aggregation Database. The arginine at codon 202 is weakly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.554). Due to conflicting information, the clinical significance of this variant is uncertain at this time. -

Jun 11, 2023
GeneDx
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Identified as a single heterozygous variant in patients with common variable immune deficiency (CVID) in the published literature; however also found at a similar frequency in controls, suggesting R202H may not contribute to risk of CVID (Salzer et al., 2005; Castigli et al., 2005; Pan-Hammarstrm et al., 2007; Freiberger et al., 2012); Published functional studies demonstrate no damaging effect, as R202H retained NF-kB activation and ligand binding (Bacchelli et al., 2011); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16007087, 16007086, 23956760, 21850030, 22884984, 19392801, 34426522, 21458042, 17392797, 30090215, 30269248, 33206719, 35655776) -

Nov 30, 2017
Eurofins Ntd Llc (ga)
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Apr 01, 2018
CeGaT Center for Human Genetics Tuebingen
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Immunodeficiency, common variable, 2 Pathogenic:1Benign:1
Jan 20, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Aug 01, 2005
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

not specified Benign:2
Jun 25, 2021
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: TNFRSF13B c.605G>A (p.Arg202His) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0008 in 249890 control chromosomes. The observed variant frequency is approximately 278.72 fold of the estimated maximal expected allele frequency for a pathogenic variant in TNFRSF13B causing Common Variable Immunodeficiency phenotype (2.9e-06), strongly suggesting that the variant is benign. c.605G>A has been reported in the literature in individuals affected with Common Variable Immunodeficiency and IgA deficiency, however without strong supporting evidence of pathogenicity and often also being found in controls (Castigli_2005, Salzar_2005, Castigli_2007, Lopez-Mejias_2009, Freiberger_2012, DeVries_2011, Karaca_2018, Pulvirenti_2016). The variant has been reported to not segregate with disease in 3 families, including the variant being found in unaffected family members and affected family members lacking the variant (Pan-Hammarstrom_2007, Speletas_2011). Experimental evidence showed the variant had little or no inhibitory effect on signaling via NF-kB and AP-1 and did not impair the interaction with MyD88, TRAF2, TRAF5, TRAF6 or CAML (He_2010). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Two labs classified the variant as benign/likely benign while two classified the variant as VUS. Based on the evidence outlined above, the variant was classified as likely benign. -

Dec 07, 2023
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.Arg202His variant in TNFRSF13B has been reported in multiple individuals with combined immunodeficiency or IgA deficiency, however it has also been found at similar frequencies in control populations and was not found to segregate with individuals in a family (Pan-Hammarstrom 2007 PMID: 17392797, Lopez-Mejias 2009 PMID: 19392801, Janzi 2012 PMID: 21850030, Speletas 2013 PMID: 23956760, van Schouwenburg 2015 PMID: 26122175). This variant has been identified in 0.14% (5/3468) of Ashkenazi Jewish and 0.1% (81/68030) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v 3.1.2). This variant has also been reported in ClinVar (Variation ID 5304). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In vitro functional studies provide some evidence that this variant does not impact protein function (Bacchelli 2011 PMID: 21458042, He 2010 PMID: 20676093); however, these types of assays may not accurately represent biological function. In summary, while the clinical significance of this variant is uncertain, these data suggest that it is more likely to be benign/its frequency suggests that it is more likely to be benign. ACMG/AMP Criteria applied: BS3_Moderate, BS4_Supporting. -

Common Variable Immune Deficiency, Dominant Benign:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Uncertain
0.010
CADD
Benign
16
DANN
Benign
0.72
DEOGEN2
Benign
0.19
T;.
Eigen
Benign
-0.82
Eigen_PC
Benign
-0.90
FATHMM_MKL
Benign
0.067
N
LIST_S2
Benign
0.56
T;T
M_CAP
Benign
0.042
D
MetaRNN
Benign
0.24
T;T
MetaSVM
Uncertain
-0.059
T
MutationAssessor
Benign
0.34
N;.
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-0.69
N;.
REVEL
Uncertain
0.55
Sift
Benign
0.20
T;.
Sift4G
Benign
0.15
T;T
Polyphen
0.47
P;B
Vest4
0.27
MVP
0.70
MPC
0.033
ClinPred
0.0097
T
GERP RS
2.0
Varity_R
0.058
gMVP
0.086

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs104894649; hg19: chr17-16843666; API