rs35062843
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_012452.3(TNFRSF13B):āc.291T>Gā(p.Pro97=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0412 in 1,614,174 control chromosomes in the GnomAD database, including 1,679 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.037 ( 125 hom., cov: 32)
Exomes š: 0.042 ( 1554 hom. )
Consequence
TNFRSF13B
NM_012452.3 synonymous
NM_012452.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.313
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 17-16948892-A-C is Benign according to our data. Variant chr17-16948892-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 260258.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-16948892-A-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.313 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0965 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF13B | NM_012452.3 | c.291T>G | p.Pro97= | synonymous_variant | 3/5 | ENST00000261652.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF13B | ENST00000261652.7 | c.291T>G | p.Pro97= | synonymous_variant | 3/5 | 1 | NM_012452.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0365 AC: 5561AN: 152176Hom.: 121 Cov.: 32
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GnomAD3 exomes AF: 0.0415 AC: 10448AN: 251480Hom.: 324 AF XY: 0.0443 AC XY: 6018AN XY: 135910
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GnomAD4 exome AF: 0.0417 AC: 61000AN: 1461880Hom.: 1554 Cov.: 36 AF XY: 0.0434 AC XY: 31551AN XY: 727240
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GnomAD4 genome ? AF: 0.0366 AC: 5572AN: 152294Hom.: 125 Cov.: 32 AF XY: 0.0375 AC XY: 2795AN XY: 74480
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 13, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Immunodeficiency, common variable, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Common Variable Immune Deficiency, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at