chr22-37510255-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014550.4(CARD10):c.866G>A(p.Arg289Gln) variant causes a missense change. The variant allele was found at a frequency of 0.188 in 1,603,122 control chromosomes in the GnomAD database, including 29,101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.20 ( 3179 hom., cov: 32)
Exomes 𝑓: 0.19 ( 25922 hom. )
Consequence
CARD10
NM_014550.4 missense
NM_014550.4 missense
Scores
1
3
13
Clinical Significance
Conservation
PhyloP100: 4.08
Genes affected
CARD10 (HGNC:16422): (caspase recruitment domain family member 10) The caspase recruitment domain (CARD) is a protein module that consists of 6 or 7 antiparallel alpha helices. It participates in apoptosis signaling through highly specific protein-protein homophilic interactions. Like several other CARD proteins, CARD10 belongs to the membrane-associated guanylate kinase (MAGUK) family and activates NF-kappa-B (NFKB; see MIM 164011) through BCL10 (MIM 603517) (Wang et al., 2001 [PubMed 11259443]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.002108544).
BP6
Variant 22-37510255-C-T is Benign according to our data. Variant chr22-37510255-C-T is described in ClinVar as [Benign]. Clinvar id is 3060680.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARD10 | NM_014550.4 | c.866G>A | p.Arg289Gln | missense_variant | 4/20 | ENST00000251973.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARD10 | ENST00000251973.10 | c.866G>A | p.Arg289Gln | missense_variant | 4/20 | 1 | NM_014550.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.200 AC: 30446AN: 151858Hom.: 3177 Cov.: 32
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GnomAD3 exomes AF: 0.183 AC: 43767AN: 239630Hom.: 4314 AF XY: 0.189 AC XY: 24666AN XY: 130736
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GnomAD4 exome AF: 0.186 AC: 270129AN: 1451148Hom.: 25922 Cov.: 37 AF XY: 0.188 AC XY: 135884AN XY: 722378
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GnomAD4 genome AF: 0.200 AC: 30470AN: 151974Hom.: 3179 Cov.: 32 AF XY: 0.201 AC XY: 14967AN XY: 74330
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CARD10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 08, 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
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
D;D
Vest4
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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