rs751285038
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000879.3(IL5):c.88G>A(p.Val30Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000743 in 1,614,070 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000879.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL5 | NM_000879.3 | c.88G>A | p.Val30Met | missense_variant | Exon 1 of 4 | ENST00000231454.6 | NP_000870.1 | |
IL5 | XM_005271988.5 | c.154G>A | p.Val52Met | missense_variant | Exon 2 of 5 | XP_005272045.1 | ||
IL5 | XM_011543373.4 | c.88G>A | p.Val30Met | missense_variant | Exon 3 of 6 | XP_011541675.1 | ||
IL5 | XM_047417148.1 | c.43-265G>A | intron_variant | Intron 1 of 3 | XP_047273104.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL5 | ENST00000231454.6 | c.88G>A | p.Val30Met | missense_variant | Exon 1 of 4 | 1 | NM_000879.3 | ENSP00000231454.1 | ||
ENSG00000283782 | ENST00000640655.2 | c.-168-15893C>T | intron_variant | Intron 2 of 25 | 5 | ENSP00000491596.2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152214Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251372Hom.: 1 AF XY: 0.00000736 AC XY: 1AN XY: 135862
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727228
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152214Hom.: 1 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.88G>A (p.V30M) alteration is located in exon 1 (coding exon 1) of the IL5 gene. This alteration results from a G to A substitution at nucleotide position 88, causing the valine (V) at amino acid position 30 to be replaced by a methionine (M). 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