chr22-49998060-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001371417.1(IL17REL):c.1000C>T(p.Pro334Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000126 in 1,593,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001371417.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17REL | NM_001371417.1 | c.1000C>T | p.Pro334Ser | missense_variant | 11/15 | ENST00000695950.1 | |
IL17REL | NM_001371416.1 | c.1000C>T | p.Pro334Ser | missense_variant | 11/15 | ||
IL17REL | NM_001001694.3 | c.784C>T | p.Pro262Ser | missense_variant | 11/15 | ||
IL17REL | XR_001755245.2 | n.1119C>T | non_coding_transcript_exon_variant | 11/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17REL | ENST00000695950.1 | c.1000C>T | p.Pro334Ser | missense_variant | 11/15 | NM_001371417.1 | A2 | ||
IL17REL | ENST00000695951.1 | c.1000C>T | p.Pro334Ser | missense_variant | 11/15 | P2 | |||
IL17REL | ENST00000389983.7 | c.*919C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000443 AC: 1AN: 225764Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 123734
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1441114Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 717216
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 22, 2021 | The c.784C>T (p.P262S) alteration is located in exon 11 (coding exon 8) of the IL17REL gene. This alteration results from a C to T substitution at nucleotide position 784, causing the proline (P) at amino acid position 262 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at