rs3917924

Variant names:

• chr1-36480052-G-A
• rs3917924
• NM_000760.4:c.-20-536C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-36480052-G-A
• chr1-36480052-G-C

Variant summary

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

The NM_000760.4(CSF3R):​c.-20-536C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 204,150 control chromosomes in the GnomAD database, including 12,931 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 0.33 (9243 hom., cov: 32)
  • Exomes 𝑓: 0.37 (3688 hom.)
• Consequence: CSF3R NM_000760.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

Genes affected

CSF3R (HGNC:2439): (colony stimulating factor 3 receptor) The protein encoded by this gene is the receptor for colony stimulating factor 3, a cytokine that controls the production, differentiation, and function of granulocytes. The encoded protein, which is a member of the family of cytokine receptors, may also function in some cell surface adhesion or recognition processes. Alternatively spliced transcript variants have been described. Mutations in this gene are a cause of Kostmann syndrome, also known as severe congenital neutropenia. [provided by RefSeq, Aug 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSF3R	NM_000760.4	c.-20-536C>T		intron_variant	Intron 2 of 16	ENST00000373106.6	NP_000751.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSF3R	ENST00000373106.6	c.-20-536C>T		intron_variant	Intron 2 of 16	1	NM_000760.4	ENSP00000362198.2

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50341 AN: 151982 Hom.: 9243 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.365 AC: 19019 AN: 52050 Hom.: 3688 Cov.: 0 AF XY: 0.370 AC XY: 10133 AN XY: 27402

Gnomad4 AFR exome AF: 0.187

Gnomad4 AMR exome AF: 0.479

Gnomad4 ASJ exome AF: 0.396

Gnomad4 EAS exome AF: 0.0999

Gnomad4 SAS exome AF: 0.435

Gnomad4 FIN exome AF: 0.383

Gnomad4 NFE exome AF: 0.373

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.331 AC: 50355 AN: 152100 Hom.: 9243 Cov.: 32 AF XY: 0.333 AC XY: 24797 AN XY: 74354

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.333

Alfa AF: 0.386 Hom.: 16614

Bravo AF: 0.325

Asia WGS AF: 0.262 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.8
DANN	Benign	0.69

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: rs3917924; hg19: chr1-36945653;