rs577890523
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PP5_ModerateBP4BS2_Supporting
The NM_017563.5(IL17RD):c.676G>A(p.Gly226Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000248 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
IL17RD
NM_017563.5 missense
NM_017563.5 missense
Scores
2
6
11
Clinical Significance
Conservation
PhyloP100: 5.81
Genes affected
IL17RD (HGNC:17616): (interleukin 17 receptor D) This gene encodes a membrane protein belonging to the interleukin-17 receptor (IL-17R) protein family. The encoded protein is a component of the interleukin-17 receptor signaling complex, and the interaction between this protein and IL-17R does not require the interleukin. The gene product also affects fibroblast growth factor signaling, inhibiting or stimulating growth through MAPK/ERK signaling. Alternate splicing generates multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PP5
?
Variant 3-57105928-C-T is Pathogenic according to our data. Variant chr3-57105928-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 545109.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr3-57105928-C-T is described in Lovd as [Likely_pathogenic].
BP4
?
Computational evidence support a benign effect (MetaRNN=0.1326899). . Strength limited to SUPPORTING due to the PP5.
BS2
?
High AC in GnomAd4 at 10 AD,Digenic gene. Variant has AC lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RD | NM_017563.5 | c.676G>A | p.Gly226Ser | missense_variant | 7/13 | ENST00000296318.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RD | ENST00000296318.12 | c.676G>A | p.Gly226Ser | missense_variant | 7/13 | 1 | NM_017563.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152034Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251024Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135674
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GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461634Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727106
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GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152152Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74374
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ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cerebral arteriovenous malformation Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital | Feb 14, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;.;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;.
REVEL
Benign
Sift
Uncertain
D;D;D;.
Sift4G
Pathogenic
D;D;D;.
Polyphen
D;.;.;.
Vest4
MutPred
Loss of catalytic residue at P222 (P = 0.0914);.;.;.;
MVP
MPC
ClinPred
T
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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