rs144383122
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_012452.3(TNFRSF13B):āc.828C>Gā(p.Asp276Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,613,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_012452.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF13B | NM_012452.3 | c.828C>G | p.Asp276Glu | missense_variant | 5/5 | ENST00000261652.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF13B | ENST00000261652.7 | c.828C>G | p.Asp276Glu | missense_variant | 5/5 | 1 | NM_012452.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000563 AC: 14AN: 248842Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134676
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1461350Hom.: 0 Cov.: 37 AF XY: 0.0000234 AC XY: 17AN XY: 726946
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74466
ClinVar
Submissions by phenotype
Immunodeficiency, common variable, 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 18, 2022 | This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 276 of the TNFRSF13B protein (p.Asp276Glu). This variant is present in population databases (rs144383122, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with TNFRSF13B-related conditions. ClinVar contains an entry for this variant (Variation ID: 538710). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TNFRSF13B protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at