NM_000879.3:c.49G>A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000879.3(IL5):c.49G>A(p.Val17Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,060 control chromosomes in the GnomAD database, including 1 homozygotes. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000879.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL5 | NM_000879.3 | c.49G>A | p.Val17Met | missense_variant | Exon 1 of 4 | ENST00000231454.6 | NP_000870.1 | |
IL5 | XM_005271988.5 | c.115G>A | p.Val39Met | missense_variant | Exon 2 of 5 | XP_005272045.1 | ||
IL5 | XM_011543373.4 | c.49G>A | p.Val17Met | missense_variant | Exon 3 of 6 | XP_011541675.1 | ||
IL5 | XM_047417148.1 | c.43-304G>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.49G>A | p.Val17Met | missense_variant | Exon 1 of 4 | 1 | NM_000879.3 | ENSP00000231454.1 | ||
ENSG00000283782 | ENST00000638452.2 | c.-168-15854C>T | intron_variant | Intron 3 of 26 | 5 | ENSP00000492349.2 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152226Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000279 AC: 7AN: 251288 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461716Hom.: 1 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727174 show subpopulations
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74494 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at