NM_012452.3:c.*86_*88delTGA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_012452.3(TNFRSF13B):c.*86_*88delTGA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 1,444,368 control chromosomes in the GnomAD database, including 1,847 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_012452.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0383 AC: 5790AN: 151350Hom.: 206 Cov.: 29
GnomAD4 exome AF: 0.0390 AC: 50387AN: 1292900Hom.: 1641 AF XY: 0.0404 AC XY: 25599AN XY: 634112
GnomAD4 genome AF: 0.0383 AC: 5794AN: 151468Hom.: 206 Cov.: 29 AF XY: 0.0388 AC XY: 2875AN XY: 74008
ClinVar
Submissions by phenotype
not specified Benign:1
Variant summary: TNFRSF13B c.*86_*88delTGA is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.04 in 31156 control chromosomes in the gnomAD database, including 49 homozygotes. The observed variant frequency is approximately 14076 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. To our knowledge, no occurrence of c.*86_*88delTGA in individuals affected with Common Variable Immunodeficiency and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign. -
Immunodeficiency, common variable, 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at