rs5771069
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001371417.1(IL17REL):āc.1281T>Cā(p.Ala427=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,558,162 control chromosomes in the GnomAD database, including 220,840 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.55 ( 23630 hom., cov: 34)
Exomes š: 0.52 ( 197210 hom. )
Consequence
IL17REL
NM_001371417.1 synonymous
NM_001371417.1 synonymous
Scores
18
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.83
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=1.0144996E-6).
BP7
Synonymous conserved (PhyloP=-4.82 with no splicing effect.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL17REL | NM_001371417.1 | c.1281T>C | p.Ala427= | synonymous_variant | 14/15 | ENST00000695950.1 | |
IL17REL | NM_001371416.1 | c.1214T>C | p.Leu405Pro | missense_variant | 14/15 | ||
IL17REL | NM_001001694.3 | c.998T>C | p.Leu333Pro | missense_variant | 14/15 | ||
IL17REL | XR_001755245.2 | n.1400T>C | non_coding_transcript_exon_variant | 14/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL17REL | ENST00000695950.1 | c.1281T>C | p.Ala427= | synonymous_variant | 14/15 | NM_001371417.1 | A2 | ||
IL17REL | ENST00000695951.1 | c.1214T>C | p.Leu405Pro | missense_variant | 14/15 | P2 | |||
IL17REL | ENST00000389983.7 | c.*1133T>C | 3_prime_UTR_variant, NMD_transcript_variant | 14/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.552 AC: 83926AN: 151954Hom.: 23604 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.564 AC: 104593AN: 185426Hom.: 30121 AF XY: 0.569 AC XY: 56978AN XY: 100172
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GnomAD4 exome AF: 0.525 AC: 738064AN: 1406090Hom.: 197210 Cov.: 38 AF XY: 0.531 AC XY: 370033AN XY: 696380
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GnomAD4 genome AF: 0.552 AC: 84008AN: 152072Hom.: 23630 Cov.: 34 AF XY: 0.558 AC XY: 41492AN XY: 74344
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1937
ESP6500AA
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Asia WGS
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MPC
0.35
ClinPred
T
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at