5-132060639-C-T

Variant names:

• chr5-132060639-C-T
• rs31480
• ENST00000791953.1:n.85+2001G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000791953.1(ENSG00000303119):​n.85+2001G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000303119 ENST00000791953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 24 publications found

Genes affected

ENSG00000303119 (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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105379174	XR_001742531.2	n.211+832G>A		intron_variant	Intron 2 of 4
LOC105379174	XR_948784.3	n.398+832G>A		intron_variant	Intron 2 of 2
LOC105379174	XR_948785.3	n.228+832G>A		intron_variant	Intron 2 of 4
IL3	NM_000588.4	c.-68C>T		upstream_gene_variant		ENST00000296870.3	NP_000579.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.120 AC: 3917 AN: 32628

American (AMR) AF: 0.228 AC: 9700 AN: 42462

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 5676 AN: 24770

East Asian (EAS) AF: 0.536 AC: 21051 AN: 39244

South Asian (SAS) AF: 0.257 AC: 21530 AN: 83690

European-Finnish (FIN) AF: 0.317 AC: 15643 AN: 49350

Middle Eastern (MID) AF: 0.169 AC: 685 AN: 4060

European-Non Finnish (NFE) AF: 0.215 AC: 236334 AN: 1096824

Other (OTH) AF: 0.231 AC: 13666 AN: 59058

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

African (AFR) AF: 0.117 AC: 4861 AN: 41462

American (AMR) AF: 0.205 AC: 3125 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3466

East Asian (EAS) AF: 0.541 AC: 2772 AN: 5128

South Asian (SAS) AF: 0.279 AC: 1341 AN: 4806

European-Finnish (FIN) AF: 0.322 AC: 3397 AN: 10558

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15135 AN: 67936

Other (OTH) AF: 0.202 AC: 427 AN: 2110

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
PhyloP100		0.47
PromoterAI		-0.028	Neutral
Mutation Taster		=298/2	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: rs31480; hg19: chr5-131396332; COSMIC: COSV57308776;