5-132062781-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000588.4(IL3):c.449C>T(p.Ala150Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,258 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A150T) has been classified as Uncertain significance.
Frequency
Consequence
NM_000588.4 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 |
---|---|---|---|---|---|---|---|---|
IL3 | NM_000588.4 | c.449C>T | p.Ala150Val | missense_variant | Exon 5 of 5 | ENST00000296870.3 | NP_000579.2 | |
LOC105379174 | XR_948784.3 | n.111G>A | non_coding_transcript_exon_variant | Exon 1 of 3 | ||||
LOC105379174 | XR_001742531.2 | n.-69G>A | upstream_gene_variant | |||||
LOC105379174 | XR_948785.3 | n.-60G>A | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251234Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135796
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1460944Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 726604
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.449C>T (p.A150V) alteration is located in exon 5 (coding exon 5) of the IL3 gene. This alteration results from a C to T substitution at nucleotide position 449, causing the alanine (A) at amino acid position 150 to be replaced by a valine (V). 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