20-46118343-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001250.6(CD40):c.-1T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 1,613,190 control chromosomes in the GnomAD database, including 461,294 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001250.6 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD40 | NM_001250.6 | c.-1T>C | 5_prime_UTR_variant | Exon 1 of 9 | ENST00000372285.8 | NP_001241.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.792 AC: 120443AN: 152090Hom.: 48449 Cov.: 34
GnomAD3 exomes AF: 0.748 AC: 187810AN: 251134Hom.: 71019 AF XY: 0.743 AC XY: 100891AN XY: 135764
GnomAD4 exome AF: 0.750 AC: 1095784AN: 1460982Hom.: 412773 Cov.: 47 AF XY: 0.749 AC XY: 544217AN XY: 726826
GnomAD4 genome AF: 0.792 AC: 120577AN: 152208Hom.: 48521 Cov.: 34 AF XY: 0.787 AC XY: 58533AN XY: 74408
ClinVar
Submissions by phenotype
Hyper-IgM syndrome type 3 Benign:4
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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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 95% of patients studied by a panel of primary immunodeficiencies. Number of patients: 90. Only high quality variants are reported. -
not provided Benign:3
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This variant is associated with the following publications: (PMID: 20137882, 18287517, 20127135, 21091218, 17344890, 20473910, 23669336, 18097708, 20634952, 24828072, 15731360, 27745838, 29780830, 31373353, 31642196, 23954880) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at