7-2945952-C-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_032415.7(CARD11):āc.225G>Cā(p.Arg75Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 1,613,940 control chromosomes in the GnomAD database, including 1,292 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.056 ( 616 hom., cov: 32)
Exomes š: 0.016 ( 676 hom. )
Consequence
CARD11
NM_032415.7 synonymous
NM_032415.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.32
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 Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 7-2945952-C-G is Benign according to our data. Variant chr7-2945952-C-G is described in ClinVar as [Benign]. Clinvar id is 473930.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.32 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CARD11 | NM_032415.7 | c.225G>C | p.Arg75Arg | synonymous_variant | 4/25 | ENST00000396946.9 | NP_115791.3 | |
CARD11 | NM_001324281.3 | c.225G>C | p.Arg75Arg | synonymous_variant | 5/26 | NP_001311210.1 | ||
CARD11-AS1 | NR_187443.1 | n.475-645C>G | intron_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0556 AC: 8463AN: 152094Hom.: 612 Cov.: 32
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GnomAD3 exomes AF: 0.0212 AC: 5322AN: 251296Hom.: 278 AF XY: 0.0179 AC XY: 2437AN XY: 135808
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GnomAD4 exome AF: 0.0156 AC: 22850AN: 1461728Hom.: 676 Cov.: 32 AF XY: 0.0146 AC XY: 10625AN XY: 727150
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GnomAD4 genome AF: 0.0558 AC: 8487AN: 152212Hom.: 616 Cov.: 32 AF XY: 0.0549 AC XY: 4084AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Severe combined immunodeficiency due to CARD11 deficiency;C4551967:BENTA disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
CARD11-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 02, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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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