rs1801275
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000418(IL4R):c.1727A>G(p.Gln576Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152070 control chromosomes in the gnomAD Genomes database, including 12686 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
Frequency
Genomes: 𝑓 0.35 ( 12686 hom., cov: 33)
Exomes 𝑓: 0.25 ( 9564 hom. )
Consequence
IL4R
NM_000418 missense
NM_000418 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: 1.05
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.1686489E-6).
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL4R | NM_000418.4 | c.1727A>G | p.Gln576Arg | missense_variant | 11/11 | ENST00000395762.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL4R | ENST00000395762.7 | c.1727A>G | p.Gln576Arg | missense_variant | 11/11 | 1 | NM_000418.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.347 AC: 52747AN: 152070Hom.: 12686 Cov.: 33
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33
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GnomAD3 exomes AF: 0.248 AC: 61954AN: 250126Hom.: 9564 AF XY: 0.235 AC XY: 31920AN XY: 135542
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GnomAD4 exome AF: 0.225 AC: 328389AN: 1461722Hom.: 41529 AF XY: 0.222 AC XY: 161640AN XY: 727180
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TwinsUK
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781
ALSPAC
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829
ESP6500AA
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2963
ESP6500EA
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1753
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30865
Asia WGS
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967
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ClinVar
Significance: risk factor
Submissions summary: Benign:1Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Atopy, resistance to Benign:1Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Oct 09, 2023 | - - |
Benign, no assertion criteria provided | literature only | OMIM | Feb 01, 2005 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.
MutationTaster
Benign
P;P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N;.
REVEL
Benign
Sift
Benign
T;T;.
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at