12-66211448-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_007199.3(IRAK3):ā€‹c.439A>Gā€‹(p.Ile147Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 1,589,414 control chromosomes in the GnomAD database, including 652,620 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: š‘“ 0.79 ( 50526 hom., cov: 32)
Exomes š‘“: 0.91 ( 602094 hom. )

Consequence

IRAK3
NM_007199.3 missense, splice_region

Scores

18

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.420
Variant links:
Genes affected
IRAK3 (HGNC:17020): (interleukin 1 receptor associated kinase 3) This gene encodes a member of the interleukin-1 receptor-associated kinase protein family. Members of this family are essential components of the Toll/IL-R immune signal transduction pathways. This protein is primarily expressed in monocytes and macrophages and functions as a negative regulator of Toll-like receptor signaling. Mutations in this gene are associated with a susceptibility to asthma. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=6.8947065E-7).
BP6
Variant 12-66211448-A-G is Benign according to our data. Variant chr12-66211448-A-G is described in ClinVar as [Benign]. Clinvar id is 3059815.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IRAK3NM_007199.3 linkuse as main transcriptc.439A>G p.Ile147Val missense_variant, splice_region_variant 5/12 ENST00000261233.9
IRAK3NM_001142523.2 linkuse as main transcriptc.256A>G p.Ile86Val missense_variant, splice_region_variant 4/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IRAK3ENST00000261233.9 linkuse as main transcriptc.439A>G p.Ile147Val missense_variant, splice_region_variant 5/121 NM_007199.3 P1Q9Y616-1
IRAK3ENST00000457197.2 linkuse as main transcriptc.256A>G p.Ile86Val missense_variant, splice_region_variant 4/112 Q9Y616-2

Frequencies

GnomAD3 genomes
AF:
0.790
AC:
120057
AN:
152054
Hom.:
50509
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.480
Gnomad AMI
AF:
0.838
Gnomad AMR
AF:
0.897
Gnomad ASJ
AF:
0.937
Gnomad EAS
AF:
0.600
Gnomad SAS
AF:
0.869
Gnomad FIN
AF:
0.914
Gnomad MID
AF:
0.886
Gnomad NFE
AF:
0.933
Gnomad OTH
AF:
0.827
GnomAD3 exomes
AF:
0.872
AC:
218441
AN:
250616
Hom.:
97642
AF XY:
0.879
AC XY:
119179
AN XY:
135570
show subpopulations
Gnomad AFR exome
AF:
0.472
Gnomad AMR exome
AF:
0.945
Gnomad ASJ exome
AF:
0.935
Gnomad EAS exome
AF:
0.597
Gnomad SAS exome
AF:
0.890
Gnomad FIN exome
AF:
0.911
Gnomad NFE exome
AF:
0.931
Gnomad OTH exome
AF:
0.896
GnomAD4 exome
AF:
0.911
AC:
1308715
AN:
1437242
Hom.:
602094
Cov.:
29
AF XY:
0.911
AC XY:
652923
AN XY:
716676
show subpopulations
Gnomad4 AFR exome
AF:
0.467
Gnomad4 AMR exome
AF:
0.938
Gnomad4 ASJ exome
AF:
0.938
Gnomad4 EAS exome
AF:
0.592
Gnomad4 SAS exome
AF:
0.888
Gnomad4 FIN exome
AF:
0.911
Gnomad4 NFE exome
AF:
0.937
Gnomad4 OTH exome
AF:
0.881
GnomAD4 genome
AF:
0.789
AC:
120113
AN:
152172
Hom.:
50526
Cov.:
32
AF XY:
0.791
AC XY:
58830
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.480
Gnomad4 AMR
AF:
0.897
Gnomad4 ASJ
AF:
0.937
Gnomad4 EAS
AF:
0.600
Gnomad4 SAS
AF:
0.869
Gnomad4 FIN
AF:
0.914
Gnomad4 NFE
AF:
0.933
Gnomad4 OTH
AF:
0.828
Alfa
AF:
0.904
Hom.:
151744
Bravo
AF:
0.773
TwinsUK
AF:
0.944
AC:
3502
ALSPAC
AF:
0.937
AC:
3611
ESP6500AA
AF:
0.493
AC:
2170
ESP6500EA
AF:
0.933
AC:
8022
ExAC
AF:
0.862
AC:
104622
Asia WGS
AF:
0.726
AC:
2527
AN:
3478
EpiCase
AF:
0.933
EpiControl
AF:
0.926

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

IRAK3-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesOct 17, 2019This 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.68
T
BayesDel_noAF
Benign
-0.60
CADD
Benign
0.49
DANN
Benign
0.23
DEOGEN2
Benign
0.050
T;.
Eigen
Benign
-0.88
Eigen_PC
Benign
-0.88
FATHMM_MKL
Benign
0.045
N
LIST_S2
Benign
0.42
T;T
MetaRNN
Benign
6.9e-7
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
2.0
M;.
MutationTaster
Benign
1.0
P;P
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.18
N;N
REVEL
Benign
0.033
Sift
Benign
0.61
T;T
Sift4G
Benign
0.14
T;T
Polyphen
0.0010
B;B
Vest4
0.027
MPC
0.021
ClinPred
0.0014
T
GERP RS
0.74
Varity_R
0.028
gMVP
0.13

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs1152888; hg19: chr12-66605228; COSMIC: COSV54160564; API