chr22-49999915-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001371417.1(IL17REL):āc.603A>Gā(p.Gln201=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000333 in 1,535,396 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0018 ( 1 hom., cov: 33)
Exomes š: 0.00017 ( 2 hom. )
Consequence
IL17REL
NM_001371417.1 synonymous
NM_001371417.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.299
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 22-49999915-T-C is Benign according to our data. Variant chr22-49999915-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2653360.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.299 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17REL | NM_001371417.1 | c.603A>G | p.Gln201= | synonymous_variant | 7/15 | ENST00000695950.1 | |
IL17REL | NM_001371416.1 | c.603A>G | p.Gln201= | synonymous_variant | 7/15 | ||
IL17REL | NM_001001694.3 | c.387A>G | p.Gln129= | synonymous_variant | 7/15 | ||
IL17REL | XR_001755245.2 | n.722A>G | non_coding_transcript_exon_variant | 7/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17REL | ENST00000695950.1 | c.603A>G | p.Gln201= | synonymous_variant | 7/15 | NM_001371417.1 | A2 | ||
IL17REL | ENST00000695951.1 | c.603A>G | p.Gln201= | synonymous_variant | 7/15 | P2 | |||
IL17REL | ENST00000389983.7 | c.*522A>G | 3_prime_UTR_variant, NMD_transcript_variant | 7/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00171 AC: 259AN: 151884Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000462 AC: 63AN: 136348Hom.: 1 AF XY: 0.000411 AC XY: 30AN XY: 72990
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GnomAD4 exome AF: 0.000171 AC: 236AN: 1383392Hom.: 2 Cov.: 31 AF XY: 0.000149 AC XY: 102AN XY: 682314
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GnomAD4 genome AF: 0.00182 AC: 276AN: 152004Hom.: 1 Cov.: 33 AF XY: 0.00175 AC XY: 130AN XY: 74310
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | IL17REL: BP4, BP7 - |
Computational scores
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Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at