rs31481

Variant names:

• chr5-132061509-G-A
• rs31481
• NM_000588.4:c.204+501G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-132061509-G-A
• chr5-132061509-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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]

ENSG00000303119 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IL3	NM_000588.4	c.204+501G>A		intron_variant	Intron 2 of 4	ENST00000296870.3	NP_000579.2
LOC105379174	XR_001742531.2	n.173C>T		non_coding_transcript_exon_variant	Exon 2 of 5
LOC105379174	XR_948784.3	n.360C>T		non_coding_transcript_exon_variant	Exon 2 of 3
LOC105379174	XR_948785.3	n.190C>T		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL3	ENST00000296870.3	c.204+501G>A		intron_variant	Intron 2 of 4	1	NM_000588.4	ENSP00000296870.2

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

African (AFR) AF: 0.174 AC: 7231 AN: 41488

American (AMR) AF: 0.192 AC: 2935 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3468

East Asian (EAS) AF: 0.541 AC: 2793 AN: 5160

South Asian (SAS) AF: 0.266 AC: 1286 AN: 4828

European-Finnish (FIN) AF: 0.250 AC: 2637 AN: 10560

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11695 AN: 67990

Other (OTH) AF: 0.196 AC: 414 AN: 2110

Alfa AF: 0.189 Hom.: 513

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
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs31481; hg19: chr5-131397202;