17-16939598-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_012452.3(TNFRSF13B):c.831T>C(p.Ser277Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 1,612,726 control chromosomes in the GnomAD database, including 168,814 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_012452.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.495 AC: 75120AN: 151718Hom.: 19662 Cov.: 31
GnomAD3 exomes AF: 0.495 AC: 122856AN: 248314Hom.: 32451 AF XY: 0.492 AC XY: 66151AN XY: 134406
GnomAD4 exome AF: 0.442 AC: 645265AN: 1460890Hom.: 149108 Cov.: 52 AF XY: 0.446 AC XY: 324418AN XY: 726644
GnomAD4 genome AF: 0.495 AC: 75222AN: 151836Hom.: 19706 Cov.: 31 AF XY: 0.499 AC XY: 36977AN XY: 74172
ClinVar
Submissions by phenotype
not specified Benign:3
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
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This variant is classified as Benign based on local population frequency. This variant was detected in 68% of patients studied by a panel of primary immunodeficiencies. Number of patients: 65. Only high quality variants are reported. -
not provided Benign:2Other:1
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Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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Immunodeficiency, common variable, 2 Benign:2
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Common Variable Immune Deficiency, Dominant Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at