chr7-2906705-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP6_Moderate
The NM_032415.7(CARD11):c.3398G>A(p.Arg1133His) variant causes a missense change. The variant allele was found at a frequency of 0.0000638 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R1133R) has been classified as Benign.
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000067 ( 0 hom. )
Consequence
CARD11
NM_032415.7 missense
NM_032415.7 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 3.76
Genes affected
CARD11 (HGNC:16393): (caspase recruitment domain family member 11) The protein encoded by this gene belongs to the membrane-associated guanylate kinase (MAGUK) family, a class of proteins that functions as molecular scaffolds for the assembly of multiprotein complexes at specialized regions of the plasma membrane. This protein is also a member of the CARD protein family, which is defined by carrying a characteristic caspase-associated recruitment domain (CARD). This protein has a domain structure similar to that of CARD14 protein. The CARD domains of both proteins have been shown to specifically interact with BCL10, a protein known to function as a positive regulator of cell apoptosis and NF-kappaB activation. When expressed in cells, this protein activated NF-kappaB and induced the phosphorylation of BCL10. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, CARD11
BP6
?
Variant 7-2906705-C-T is Benign according to our data. Variant chr7-2906705-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 657094.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.3398G>A | p.Arg1133His | missense_variant | 25/25 | ENST00000396946.9 | |
CARD11 | NM_001324281.3 | c.3398G>A | p.Arg1133His | missense_variant | 26/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD11 | ENST00000396946.9 | c.3398G>A | p.Arg1133His | missense_variant | 25/25 | 1 | NM_032415.7 | P1 | |
CARD11 | ENST00000698637.1 | n.4508G>A | non_coding_transcript_exon_variant | 24/24 | |||||
CARD11 | ENST00000698652.1 | n.2354G>A | non_coding_transcript_exon_variant | 8/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152252Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251188Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135850
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GnomAD4 exome AF: 0.0000670 AC: 98AN: 1461636Hom.: 0 Cov.: 30 AF XY: 0.0000619 AC XY: 45AN XY: 727130
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GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74502
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 22, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Loss of MoRF binding (P = 0.0778);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at