5-132062566-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000588.4(IL3):c.335C>T(p.Thr112Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000588.4 missense, splice_region
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.335C>T | p.Thr112Met | missense_variant, splice_region_variant | Exon 4 of 5 | ENST00000296870.3 | NP_000579.2 | |
LOC105379174 | XR_001742531.2 | n.73+74G>A | intron_variant | Intron 1 of 4 | ||||
LOC105379174 | XR_948784.3 | n.252+74G>A | intron_variant | Intron 1 of 2 | ||||
LOC105379174 | XR_948785.3 | n.82+74G>A | intron_variant | Intron 1 of 4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251490Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135920
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461838Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727234
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.335C>T (p.T112M) alteration is located in exon 4 (coding exon 4) of the IL3 gene. This alteration results from a C to T substitution at nucleotide position 335, causing the threonine (T) at amino acid position 112 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