rs1009639
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_139017.7(IL31RA):c.129C>T(p.Pro43=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 1,612,148 control chromosomes in the GnomAD database, including 418,680 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.70 ( 37265 hom., cov: 32)
Exomes 𝑓: 0.72 ( 381415 hom. )
Consequence
IL31RA
NM_139017.7 synonymous
NM_139017.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.288
Genes affected
IL31RA (HGNC:18969): (interleukin 31 receptor A) The protein encoded by this gene belongs to the type I cytokine receptor family. This receptor, with homology to gp130, is expressed on monocytes, and is involved in IL-31 signaling via activation of STAT-3 and STAT-5. It functions either as a monomer, or as part of a receptor complex with oncostatin M receptor (OSMR). Several alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 5-55859574-C-T is Benign according to our data. Variant chr5-55859574-C-T is described in ClinVar as [Benign]. Clinvar id is 1300053.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr5-55859574-C-T is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.288 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL31RA | NM_139017.7 | c.129C>T | p.Pro43= | synonymous_variant | 2/15 | ENST00000652347.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL31RA | ENST00000652347.2 | c.129C>T | p.Pro43= | synonymous_variant | 2/15 | NM_139017.7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.696 AC: 105685AN: 151948Hom.: 37245 Cov.: 32
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GnomAD3 exomes AF: 0.676 AC: 170006AN: 251414Hom.: 59806 AF XY: 0.692 AC XY: 94083AN XY: 135876
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GnomAD4 exome AF: 0.719 AC: 1049850AN: 1460080Hom.: 381415 Cov.: 38 AF XY: 0.723 AC XY: 524905AN XY: 726504
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GnomAD4 genome ? AF: 0.695 AC: 105761AN: 152068Hom.: 37265 Cov.: 32 AF XY: 0.696 AC XY: 51752AN XY: 74340
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Amyloidosis, primary localized cutaneous, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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