rs778024793
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_052945.4(TNFRSF13C):āc.264A>Gā(p.Ala88=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000066 in 1,606,422 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000039 ( 0 hom., cov: 32)
Exomes š: 0.000069 ( 3 hom. )
Consequence
TNFRSF13C
NM_052945.4 synonymous
NM_052945.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.208
Genes affected
TNFRSF13C (HGNC:17755): (TNF receptor superfamily member 13C) B cell-activating factor (BAFF) enhances B-cell survival in vitro and is a regulator of the peripheral B-cell population. Overexpression of Baff in mice results in mature B-cell hyperplasia and symptoms of systemic lupus erythematosus (SLE). Also, some SLE patients have increased levels of BAFF in serum. Therefore, it has been proposed that abnormally high levels of BAFF may contribute to the pathogenesis of autoimmune diseases by enhancing the survival of autoreactive B cells. The protein encoded by this gene is a receptor for BAFF and is a type III transmembrane protein containing a single extracellular cysteine-rich domain. It is thought that this receptor is the principal receptor required for BAFF-mediated mature B-cell survival. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 22-41926204-T-C is Benign according to our data. Variant chr22-41926204-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 471474.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.208 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF13C | NM_052945.4 | c.264A>G | p.Ala88= | synonymous_variant | 2/3 | ENST00000291232.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF13C | ENST00000291232.5 | c.264A>G | p.Ala88= | synonymous_variant | 2/3 | 1 | NM_052945.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152122Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000136 AC: 31AN: 228648Hom.: 0 AF XY: 0.000181 AC XY: 23AN XY: 127028
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GnomAD4 exome AF: 0.0000688 AC: 100AN: 1454300Hom.: 3 Cov.: 33 AF XY: 0.000101 AC XY: 73AN XY: 723636
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74326
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Immunodeficiency, common variable, 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 10, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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