chr3-57097731-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017563.5(IL17RD):c.1972A>G(p.Met658Val) variant causes a missense change. The variant allele was found at a frequency of 0.000315 in 1,602,970 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00043 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00030 ( 1 hom. )
Consequence
IL17RD
NM_017563.5 missense
NM_017563.5 missense
Scores
1
6
11
Clinical Significance
Conservation
PhyloP100: 3.82
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0065295994).
BP6
?
Variant 3-57097731-T-C is Benign according to our data. Variant chr3-57097731-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 677804.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000427 (65/152296) while in subpopulation EAS AF= 0.0116 (60/5172). AF 95% confidence interval is 0.00925. There are 0 homozygotes in gnomad4. There are 42 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 65 AD,Digenic gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RD | NM_017563.5 | c.1972A>G | p.Met658Val | missense_variant | 12/13 | ENST00000296318.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RD | ENST00000296318.12 | c.1972A>G | p.Met658Val | missense_variant | 12/13 | 1 | NM_017563.5 | P1 | |
IL17RD | ENST00000320057.9 | c.1540A>G | p.Met514Val | missense_variant | 13/14 | 1 | |||
IL17RD | ENST00000463523.5 | c.1540A>G | p.Met514Val | missense_variant | 12/13 | 1 | |||
IL17RD | ENST00000469841.5 | n.1909A>G | non_coding_transcript_exon_variant | 12/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000427 AC: 65AN: 152178Hom.: 0 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
65
AN:
152178
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00106 AC: 254AN: 239236Hom.: 1 AF XY: 0.00110 AC XY: 142AN XY: 129454
GnomAD3 exomes
AF:
AC:
254
AN:
239236
Hom.:
AF XY:
AC XY:
142
AN XY:
129454
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000303 AC: 440AN: 1450674Hom.: 1 Cov.: 32 AF XY: 0.000276 AC XY: 199AN XY: 720214
GnomAD4 exome
AF:
AC:
440
AN:
1450674
Hom.:
Cov.:
32
AF XY:
AC XY:
199
AN XY:
720214
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000427 AC: 65AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74468
GnomAD4 genome
?
AF:
AC:
65
AN:
152296
Hom.:
Cov.:
32
AF XY:
AC XY:
42
AN XY:
74468
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
?
AF:
AC:
127
Asia WGS
AF:
AC:
11
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 24, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | May 18, 2022 | - - |
IL17RD-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 18, 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
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;.;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
B;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at