3-57097590-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_017563.5(IL17RD):c.2107+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000256 in 1,565,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017563.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL17RD | ENST00000296318.12 | c.2107+6G>A | splice_region_variant, intron_variant | Intron 12 of 12 | 1 | NM_017563.5 | ENSP00000296318.7 | |||
IL17RD | ENST00000320057.9 | c.1675+6G>A | splice_region_variant, intron_variant | Intron 13 of 13 | 1 | ENSP00000322250.5 | ||||
IL17RD | ENST00000463523.5 | c.1675+6G>A | splice_region_variant, intron_variant | Intron 12 of 12 | 1 | ENSP00000417516.1 | ||||
IL17RD | ENST00000469841.5 | n.2050G>A | non_coding_transcript_exon_variant | Exon 12 of 12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000502 AC: 9AN: 179280Hom.: 0 AF XY: 0.0000841 AC XY: 8AN XY: 95176
GnomAD4 exome AF: 0.0000248 AC: 35AN: 1413126Hom.: 0 Cov.: 31 AF XY: 0.0000329 AC XY: 23AN XY: 698418
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74486
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change falls in intron 12 of the IL17RD gene. It does not directly change the encoded amino acid sequence of the IL17RD protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs766714500, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with IL17RD-related conditions. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at