chr22-17103494-CCCAGA-C
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_014339.7(IL17RA):c.769_773del(p.Pro257ArgfsTer16) variant causes a frameshift, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,126 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. P255P) has been classified as Benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_014339.7 frameshift, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17RA | NM_014339.7 | c.769_773del | p.Pro257ArgfsTer16 | frameshift_variant, splice_region_variant | 8/13 | ENST00000319363.11 | |
IL17RA | NM_001289905.2 | c.769_773del | p.Pro257ArgfsTer16 | frameshift_variant, splice_region_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17RA | ENST00000319363.11 | c.769_773del | p.Pro257ArgfsTer16 | frameshift_variant, splice_region_variant | 8/13 | 1 | NM_014339.7 | P2 | |
IL17RA | ENST00000612619.2 | c.769_773del | p.Pro257ArgfsTer16 | frameshift_variant, splice_region_variant | 8/12 | 5 | A2 | ||
IL17RA | ENST00000694951.1 | n.727_731del | splice_region_variant, non_coding_transcript_exon_variant | 6/7 | |||||
IL17RA | ENST00000694950.1 | c.*274_*278del | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 7/7 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461126Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 726858
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Immunodeficiency 51 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 19, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at