rs2227322

Variant names:

• chr17-40015415-C-A
• rs2227322
• ENST00000583218.5:c.-60C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-40015415-C-A
• chr17-40015415-C-G
• chr17-40015415-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000583218.5(CSF3):​c.-60C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CSF3 ENST00000583218.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 27 publications found

Genes affected

CSF3 (HGNC:2438): (colony stimulating factor 3) This gene encodes a member of the IL-6 superfamily of cytokines. The encoded cytokine controls the production, differentiation, and function of granulocytes. Granulocytes are a type of white blood cell that are part of the innate immune response. A modified form of this protein is commonly administered to manage chemotherapy-induced neutropenia. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, May 2020]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583218.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSF3	NM_172219.3	MANE Select	c.-60C>A		upstream_gene	N/A	NP_757373.1
	CSF3	NM_000759.4		c.-60C>A		upstream_gene	N/A	NP_000750.1
	CSF3	NM_172220.3		c.-60C>A		upstream_gene	N/A	NP_757374.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSF3	ENST00000583218.5	TSL:2	c.-60C>A		5_prime_UTR	Exon 1 of 4	ENSP00000464421.1
	CSF3	ENST00000394149.8	TSL:1 MANE Select	c.-60C>A		upstream_gene	N/A	ENSP00000377705.4
	CSF3	ENST00000225474.6	TSL:1	c.-60C>A		upstream_gene	N/A	ENSP00000225474.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	9.9
DANN	Benign	0.80
PhyloP100		0.30
PromoterAI		-0.10	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2227322; hg19: chr17-38171668;