17-16939194-T-G
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_012452.3(TNFRSF13B):c.*353A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00346 in 231,240 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 4 hom., cov: 31)
Exomes 𝑓: 0.0035 ( 0 hom. )
Consequence
TNFRSF13B
NM_012452.3 3_prime_UTR
NM_012452.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.231
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 17-16939194-T-G is Benign according to our data. Variant chr17-16939194-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 322020.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 4 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF13B | NM_012452.3 | c.*353A>C | 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 | c.*353A>C | 3_prime_UTR_variant | 5/5 | 1 | NM_012452.3 | ENSP00000261652.2 |
Frequencies
GnomAD3 genomes AF: 0.00344 AC: 523AN: 152076Hom.: 4 Cov.: 31
GnomAD3 genomes
AF:
AC:
523
AN:
152076
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00349 AC: 276AN: 79046Hom.: 0 Cov.: 0 AF XY: 0.00315 AC XY: 127AN XY: 40348
GnomAD4 exome
AF:
AC:
276
AN:
79046
Hom.:
Cov.:
0
AF XY:
AC XY:
127
AN XY:
40348
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00344 AC: 523AN: 152194Hom.: 4 Cov.: 31 AF XY: 0.00425 AC XY: 316AN XY: 74434
GnomAD4 genome
AF:
AC:
523
AN:
152194
Hom.:
Cov.:
31
AF XY:
AC XY:
316
AN XY:
74434
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Common Variable Immune Deficiency, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at