5-132679793-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000589.4(IL4):c.263G>A(p.Arg88His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,614,044 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000589.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL4 | NM_000589.4 | c.263G>A | p.Arg88His | missense_variant | Exon 3 of 4 | ENST00000231449.7 | NP_000580.1 | |
IL4 | NM_172348.3 | c.215G>A | p.Arg72His | missense_variant | Exon 2 of 3 | NP_758858.1 | ||
IL4 | NM_001354990.2 | c.364G>A | p.Ala122Thr | missense_variant | Exon 4 of 5 | NP_001341919.1 | ||
LOC105379176 | NR_134248.1 | n.500C>T | non_coding_transcript_exon_variant | Exon 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL4 | ENST00000231449.7 | c.263G>A | p.Arg88His | missense_variant | Exon 3 of 4 | 1 | NM_000589.4 | ENSP00000231449.2 | ||
IL4 | ENST00000350025.2 | c.215G>A | p.Arg72His | missense_variant | Exon 2 of 3 | 1 | ENSP00000325190.3 | |||
IL4 | ENST00000622422.1 | c.364G>A | p.Ala122Thr | missense_variant | Exon 4 of 5 | 1 | ENSP00000480581.1 | |||
IL4 | ENST00000495905.1 | n.229G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251246Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135864
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461746Hom.: 1 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727180
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.263G>A (p.R88H) alteration is located in exon 3 (coding exon 3) of the IL4 gene. This alteration results from a G to A substitution at nucleotide position 263, causing the arginine (R) at amino acid position 88 to be replaced by a histidine (H). 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