chr22-50000773-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001371417.1(IL17REL):c.371G>A(p.Arg124Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000169 in 1,594,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001371417.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17REL | NM_001371417.1 | c.371G>A | p.Arg124Gln | missense_variant | 4/15 | ENST00000695950.1 | |
IL17REL | NM_001371416.1 | c.371G>A | p.Arg124Gln | missense_variant | 4/15 | ||
IL17REL | NM_001001694.3 | c.200G>A | p.Arg67Gln | missense_variant | 5/15 | ||
IL17REL | XR_001755245.2 | n.490G>A | non_coding_transcript_exon_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17REL | ENST00000695950.1 | c.371G>A | p.Arg124Gln | missense_variant | 4/15 | NM_001371417.1 | A2 | ||
IL17REL | ENST00000695951.1 | c.371G>A | p.Arg124Gln | missense_variant | 4/15 | P2 | |||
IL17REL | ENST00000389983.7 | c.*335G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152210Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000563 AC: 13AN: 230844Hom.: 0 AF XY: 0.0000632 AC XY: 8AN XY: 126518
GnomAD4 exome AF: 0.0000139 AC: 20AN: 1441904Hom.: 0 Cov.: 33 AF XY: 0.0000140 AC XY: 10AN XY: 716258
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152328Hom.: 0 Cov.: 34 AF XY: 0.0000671 AC XY: 5AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at