5-132060639-C-T

Position:

• chr5-132060639-C-T

Variant summary

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

The variant allele was found at a frequency of 0.227 in 1,584,032 control chromosomes in the GnomAD database, including 44,766 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 0.21 (3940 hom., cov: 31)
  • Exomes 𝑓: 0.23 (40826 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

(HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL3	NM_000588.4	c.-68C>T		upstream_gene_variant		ENST00000296870.3	NP_000579.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL3	ENST00000296870.3	c.-68C>T		upstream_gene_variant		1	NM_000588.4	ENSP00000296870.2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32029 AN: 151828 Hom.: 3935 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.194

GnomAD4 exome AF: 0.229 AC: 328202 AN: 1432086 Hom.: 40826 Cov.: 31 AF XY: 0.230 AC XY: 163458 AN XY: 709920

Gnomad4 AFR exome AF: 0.120

Gnomad4 AMR exome AF: 0.228

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.536

Gnomad4 SAS exome AF: 0.257

Gnomad4 FIN exome AF: 0.317

Gnomad4 NFE exome AF: 0.215

Gnomad4 OTH exome AF: 0.231

GnomAD4 genome AF: 0.211 AC: 32045 AN: 151946 Hom.: 3940 Cov.: 31 AF XY: 0.218 AC XY: 16179 AN XY: 74270

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.202

Alfa AF: 0.221 Hom.: 495

Bravo AF: 0.198

Asia WGS AF: 0.426 AC: 1483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.83

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: rs31480; hg19: chr5-131396332; COSMIC: COSV57308776;