rs31481

chr5-132061509-G-Achr5-132061509-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000588.4(IL3):c.204+501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,110 control chromosomes in the GnomAD database, including 3,382 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3382 hom., cov: 32)
• Consequence: IL3 NM_000588.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

IL3 (HGNC:6011): (interleukin 3) The protein encoded by this gene is a potent growth promoting cytokine. This cytokine is capable of supporting the proliferation of a broad range of hematopoietic cell types. It is involved in a variety of cell activities such as cell growth, differentiation and apoptosis. This cytokine has been shown to also possess neurotrophic activity, and it may be associated with neurologic disorders. [provided by RefSeq, Jul 2008]

LOC105379174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL3	NM_000588.4	c.204+501G>A		intron_variant		ENST00000296870.3
LOC105379174	XR_001742531.2	n.173C>T		non_coding_transcript_exon_variant	2/5
LOC105379174	XR_948784.3	n.360C>T		non_coding_transcript_exon_variant	2/3
LOC105379174	XR_948785.3	n.190C>T		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL3	ENST00000296870.3	c.204+501G>A		intron_variant		1	NM_000588.4	P1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29990 AN: 151992 Hom.: 3375 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.188

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.197 AC: 30024 AN: 152110 Hom.: 3382 Cov.: 32 AF XY: 0.204 AC XY: 15199 AN XY: 74362

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.196

Alfa AF: 0.190 Hom.: 499

Bravo AF: 0.193

Asia WGS AF: 0.423 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.8
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs31481; hg19: chr5-131397202;