22-49999501-A-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001371417.1(IL17REL):c.692T>A(p.Val231Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Consequence
IL17REL
NM_001371417.1 missense, splice_region
NM_001371417.1 missense, splice_region
Scores
7
12
Splicing: ADA: 0.01525
2
Clinical Significance
Conservation
PhyloP100: -0.294
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL17REL | NM_001371417.1 | c.692T>A | p.Val231Glu | missense_variant, splice_region_variant | 8/15 | ENST00000695950.1 | NP_001358346.1 | |
IL17REL | NM_001371416.1 | c.692T>A | p.Val231Glu | missense_variant, splice_region_variant | 8/15 | NP_001358345.1 | ||
IL17REL | NM_001001694.3 | c.476T>A | p.Val159Glu | missense_variant, splice_region_variant | 8/15 | NP_001001694.2 | ||
IL17REL | XR_001755245.2 | n.811T>A | splice_region_variant, non_coding_transcript_exon_variant | 8/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL17REL | ENST00000695950.1 | c.692T>A | p.Val231Glu | missense_variant, splice_region_variant | 8/15 | NM_001371417.1 | ENSP00000512282.1 | |||
IL17REL | ENST00000695951.1 | c.692T>A | p.Val231Glu | missense_variant, splice_region_variant | 8/15 | ENSP00000512283.1 | ||||
IL17REL | ENST00000389983.7 | n.*611T>A | splice_region_variant, non_coding_transcript_exon_variant | 8/15 | 2 | ENSP00000374633.3 | ||||
IL17REL | ENST00000389983.7 | n.*611T>A | 3_prime_UTR_variant | 8/15 | 2 | ENSP00000374633.3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 35
GnomAD4 exome
Cov.:
35
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.476T>A (p.V159E) alteration is located in exon 8 (coding exon 5) of the IL17REL gene. This alteration results from a T to A substitution at nucleotide position 476, causing the valine (V) at amino acid position 159 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MutPred
Loss of sheet (P = 7e-04);Loss of sheet (P = 7e-04);
MVP
MPC
0.53
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.