rs143049136
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP2BP4_ModerateBP6
The NM_032415.7(CARD11):c.2119C>T(p.Arg707Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000795 in 1,610,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R707H) has been classified as Likely benign.
Frequency
Consequence
NM_032415.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.2119C>T | p.Arg707Cys | missense_variant | 16/25 | ENST00000396946.9 | |
CARD11 | NM_001324281.3 | c.2119C>T | p.Arg707Cys | missense_variant | 17/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.2119C>T | p.Arg707Cys | missense_variant | 16/25 | 1 | NM_032415.7 | P1 | |
CARD11 | ENST00000355508.3 | c.532C>T | p.Arg178Cys | missense_variant | 5/7 | 3 | |||
CARD11 | ENST00000698637.1 | n.2445C>T | non_coding_transcript_exon_variant | 16/24 |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152208Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000935 AC: 23AN: 246020Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 133972
GnomAD4 exome AF: 0.0000528 AC: 77AN: 1458716Hom.: 0 Cov.: 33 AF XY: 0.0000413 AC XY: 30AN XY: 725804
GnomAD4 genome ? AF: 0.000335 AC: 51AN: 152208Hom.: 0 Cov.: 34 AF XY: 0.000403 AC XY: 30AN XY: 74358
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | The c.2119C>T (p.R707C) alteration is located in exon 16 (coding exon 15) of the CARD11 gene. This alteration results from a C to T substitution at nucleotide position 2119, causing the arginine (R) at amino acid position 707 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Severe combined immunodeficiency due to CARD11 deficiency;C4539957:Immunodeficiency 11b with atopic dermatitis;C4551967:BENTA disease Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 23, 2021 | - - |
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at