rs2532502
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001242.5(CD27):c.698A>G(p.His233Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.991 in 1,614,090 control chromosomes in the GnomAD database, including 792,098 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001242.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.994 AC: 151187AN: 152162Hom.: 75112 Cov.: 31
GnomAD3 exomes AF: 0.993 AC: 249087AN: 250914Hom.: 123640 AF XY: 0.992 AC XY: 134623AN XY: 135686
GnomAD4 exome AF: 0.990 AC: 1447750AN: 1461810Hom.: 716926 Cov.: 50 AF XY: 0.990 AC XY: 720213AN XY: 727204
GnomAD4 genome AF: 0.994 AC: 151306AN: 152280Hom.: 75172 Cov.: 31 AF XY: 0.994 AC XY: 74012AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is classified as Benign based on local population frequency. This variant was detected in 100% of patients studied by a panel of primary immunodeficiencies. Number of patients: 96. Only high quality variants are reported. -
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: MAF -
Lymphoproliferative syndrome 2 Benign:2
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at