Genetic Variant CSF3:c.*690C>T (chr17-40017649-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_172219.3(CSF3):c.*690C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,010 control chromosomes in the GnomAD database, including 10,071 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 0.36 ( 10055 hom., cov: 30)

Exomes 𝑓: 0.38 ( 16 hom. )

Consequence

CSF3
NM_172219.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Publications

32 publications found

Variant links:

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]

CSF3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSF3	NM_172219.3 link	c.*690C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000394149.8	NP_757373.1	P09919-2Q8N4W3Q6FH65

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSF3	ENST00000394149.8 link	c.*690C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_172219.3	ENSP00000377705.4		P09919-2

Frequencies

GnomAD3 genomes

AF:

0.362

AC:

54933

AN:

151626

Hom.:

10038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.441

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.396

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.340

GnomAD4 exome

AF:

0.380

AC:

101

AN:

266

Hom.:

Cov.:

AF XY:

0.331

AC XY:

AN XY:

166

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.415

AC:

AN:

130

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.136

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.380

AC:

AN:

Other (OTH)

AF:

0.438

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.363

AC:

55013

AN:

151744

Hom.:

10055

Cov.:

AF XY:

0.360

AC XY:

26716

AN XY:

74148

show subpopulations

African (AFR)

AF:

0.316

AC:

13052

AN:

41348

American (AMR)

AF:

0.348

AC:

5325

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

1212

AN:

3472

East Asian (EAS)

AF:

0.441

AC:

2264

AN:

5132

South Asian (SAS)

AF:

0.259

AC:

1244

AN:

4808

European-Finnish (FIN)

AF:

0.396

AC:

4161

AN:

10508

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.391

AC:

26571

AN:

67886

Other (OTH)

AF:

0.343

AC:

723

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1733

3466

5199

6932

8665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

544

1088

1632

2176

2720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.350

Hom.:

6962

Bravo

AF:

0.358

Asia WGS

AF:

0.370

AC:

1282

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

1.2

(source)

DANN

Benign

0.56

PhyloP100

-0.065

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over