17-16939133-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_012452.3(TNFRSF13B):c.*414G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0828 in 166,062 control chromosomes in the GnomAD database, including 922 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.085 ( 871 hom., cov: 31)
Exomes 𝑓: 0.062 ( 51 hom. )
Consequence
TNFRSF13B
NM_012452.3 3_prime_UTR
NM_012452.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.63
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 17-16939133-C-T is Benign according to our data. Variant chr17-16939133-C-T is described in ClinVar as [Benign]. Clinvar id is 322018.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF13B | NM_012452.3 | c.*414G>A | 3_prime_UTR_variant | 5/5 | ENST00000261652.7 | NP_036584.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF13B | ENST00000261652.7 | c.*414G>A | 3_prime_UTR_variant | 5/5 | 1 | NM_012452.3 | ENSP00000261652 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0848 AC: 12888AN: 151966Hom.: 874 Cov.: 31
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GnomAD4 exome AF: 0.0620 AC: 866AN: 13978Hom.: 51 Cov.: 0 AF XY: 0.0638 AC XY: 448AN XY: 7024
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GnomAD4 genome AF: 0.0847 AC: 12887AN: 152084Hom.: 871 Cov.: 31 AF XY: 0.0891 AC XY: 6621AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Common Variable Immune Deficiency, Dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at