9-136364346-C-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting

The NM_052813.5(CARD9):ā€‹c.1567G>Cā€‹(p.Glu523Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00022 in 1,569,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.00012 ( 0 hom., cov: 34)
Exomes š‘“: 0.00023 ( 0 hom. )

Consequence

CARD9
NM_052813.5 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 4.42
Variant links:
Genes affected
CARD9 (HGNC:16391): (caspase recruitment domain family member 9) The protein encoded by this gene is a member of the CARD protein family, which is defined by the presence of a characteristic caspase-associated recruitment domain (CARD). CARD is a protein interaction domain known to participate in activation or suppression of CARD containing members of the caspase family, and thus plays an important regulatory role in cell apoptosis. This protein was identified by its selective association with the CARD domain of BCL10, a postive regulator of apoptosis and NF-kappaB activation, and is thought to function as a molecular scaffold for the assembly of a BCL10 signaling complex that activates NF-kappaB. Several alternatively spliced transcript variants have been observed, but their full-length nature is not clearly defined. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.18951592).
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000231 (327/1416772) while in subpopulation NFE AF= 0.000275 (300/1090350). AF 95% confidence interval is 0.000249. There are 0 homozygotes in gnomad4_exome. There are 174 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CARD9NM_052813.5 linkuse as main transcriptc.1567G>C p.Glu523Gln missense_variant 13/13 ENST00000371732.10
LOC124902309XR_007061863.1 linkuse as main transcriptn.84+894C>G intron_variant, non_coding_transcript_variant
CARD9NM_052814.4 linkuse as main transcriptc.1442-184G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CARD9ENST00000371732.10 linkuse as main transcriptc.1567G>C p.Glu523Gln missense_variant 13/131 NM_052813.5 P1Q9H257-1

Frequencies

GnomAD3 genomes
AF:
0.000118
AC:
18
AN:
152232
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000121
AC:
22
AN:
181824
Hom.:
0
AF XY:
0.000103
AC XY:
10
AN XY:
97560
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000217
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000209
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000231
AC:
327
AN:
1416772
Hom.:
0
Cov.:
32
AF XY:
0.000248
AC XY:
174
AN XY:
700928
show subpopulations
Gnomad4 AFR exome
AF:
0.0000615
Gnomad4 AMR exome
AF:
0.000208
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000124
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000275
Gnomad4 OTH exome
AF:
0.000272
GnomAD4 genome
AF:
0.000118
AC:
18
AN:
152232
Hom.:
0
Cov.:
34
AF XY:
0.000108
AC XY:
8
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.0000724
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000203
Hom.:
0
Bravo
AF:
0.000113
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000117
AC:
1
ExAC
AF:
0.0000592
AC:
7

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsAug 02, 2021The c.1567G>C (p.E523Q) alteration is located in exon 13 (coding exon 12) of the CARD9 gene. This alteration results from a G to C substitution at nucleotide position 1567, causing the glutamic acid (E) at amino acid position 523 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Predisposition to invasive fungal disease due to CARD9 deficiency Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpSep 19, 2022This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 523 of the CARD9 protein (p.Glu523Gln). This variant is present in population databases (rs144943839, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CARD9-related conditions. ClinVar contains an entry for this variant (Variation ID: 646780). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.34
T
BayesDel_noAF
Benign
-0.44
CADD
Benign
21
DANN
Benign
0.97
DEOGEN2
Benign
0.23
T
Eigen
Benign
-0.29
Eigen_PC
Benign
-0.28
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Benign
0.75
T
M_CAP
Uncertain
0.14
D
MetaRNN
Benign
0.19
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.8
L
MutationTaster
Benign
0.92
D;D
PrimateAI
Uncertain
0.50
T
PROVEAN
Benign
-0.93
N
REVEL
Benign
0.12
Sift
Benign
0.055
T
Sift4G
Uncertain
0.054
T
Polyphen
0.58
P
Vest4
0.13
MVP
0.64
MPC
0.20
ClinPred
0.061
T
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.15
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs144943839; hg19: chr9-139258798; API