rs743564

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000296871.4(CSF2):​c.327+251T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,190 control chromosomes in the GnomAD database, including 8,392 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 0.32 ( 8392 hom., cov: 34)

Consequence

CSF2
ENST00000296871.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.184
Variant links:
Genes affected
CSF2 (HGNC:2434): (colony stimulating factor 2) The protein encoded by this gene is a cytokine that controls the production, differentiation, and function of granulocytes and macrophages. The active form of the protein is found extracellularly as a homodimer. This gene has been localized to a cluster of related genes at chromosome region 5q31, which is known to be associated with interstitial deletions in the 5q- syndrome and acute myelogenous leukemia. Other genes in the cluster include those encoding interleukins 4, 5, and 13. This gene plays a role in promoting tissue inflammation. Elevated levels of cytokines, including the one produced by this gene, have been detected in SARS-CoV-2 infected patients that develop acute respiratory distress syndrome. Mice deficient in this gene or its receptor develop pulmonary alveolar proteinosis. [provided by RefSeq, Aug 2020]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CSF2NM_000758.4 linkuse as main transcriptc.327+251T>C intron_variant ENST00000296871.4 NP_000749.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CSF2ENST00000296871.4 linkuse as main transcriptc.327+251T>C intron_variant 1 NM_000758.4 ENSP00000296871 P1

Frequencies

GnomAD3 genomes
AF:
0.318
AC:
48368
AN:
152072
Hom.:
8390
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.593
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.303
Gnomad EAS
AF:
0.00327
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.259
Gnomad MID
AF:
0.209
Gnomad NFE
AF:
0.391
Gnomad OTH
AF:
0.348
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.318
AC:
48387
AN:
152190
Hom.:
8392
Cov.:
34
AF XY:
0.304
AC XY:
22615
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.276
Gnomad4 AMR
AF:
0.308
Gnomad4 ASJ
AF:
0.303
Gnomad4 EAS
AF:
0.00328
Gnomad4 SAS
AF:
0.102
Gnomad4 FIN
AF:
0.259
Gnomad4 NFE
AF:
0.391
Gnomad4 OTH
AF:
0.343
Alfa
AF:
0.362
Hom.:
2633
Bravo
AF:
0.325
Asia WGS
AF:
0.0630
AC:
218
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.5
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs743564; hg19: chr5-131410879; COSMIC: COSV51522296; COSMIC: COSV51522296; API