rs3765459
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001250.6(CD40):c.676-114G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,156,138 control chromosomes in the GnomAD database, including 31,272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001250.6 intron
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.676-114G>A | intron_variant | Intron 8 of 8 | ENST00000372285.8 | NP_001241.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.184 AC: 27985AN: 151880Hom.: 3056 Cov.: 31
GnomAD3 exomes AF: 0.220 AC: 35321AN: 160452Hom.: 4208 AF XY: 0.228 AC XY: 19707AN XY: 86452
GnomAD4 exome AF: 0.231 AC: 231901AN: 1004140Hom.: 28211 Cov.: 13 AF XY: 0.233 AC XY: 119087AN XY: 510964
GnomAD4 genome AF: 0.184 AC: 27995AN: 151998Hom.: 3061 Cov.: 31 AF XY: 0.186 AC XY: 13800AN XY: 74272
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 21% of patients studied by a panel of primary immunodeficiencies. Number of patients: 20. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at