Variant chr17-40016848-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_172219.3(CSF3):c.504G>T(p.Pro168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00509 in 1,613,386 control chromosomes in the GnomAD database, including 171 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 64 hom., cov: 33)

Exomes 𝑓: 0.0037 ( 107 hom. )

Consequence

CSF3
NM_172219.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.29

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 made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 17-40016848-G-T is Benign according to our data. Variant chr17-40016848-G-T is described in ClinVar as [Benign]. Clinvar id is 768877.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.29 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSF3	NM_172219.3 linkuse as main transcript	c.504G>T	p.Pro168=	synonymous_variant	5/5	ENST00000394149.8	NP_757373.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF3	ENST00000394149.8 linkuse as main transcript	c.504G>T	p.Pro168=	synonymous_variant	5/5	1	NM_172219.3	ENSP00000377705	A2	P09919-2

Frequencies

GnomAD3 genomes

AF:

0.0181

AC:

2759

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0559

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00792

Gnomad ASJ

AF:

0.0219

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00559

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0669

Gnomad NFE

AF:

0.00231

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.00721

AC:

1811

AN:

251164

Hom.:

AF XY:

0.00640

AC XY:

869

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.0560

Gnomad AMR exome

AF:

0.00602

Gnomad ASJ exome

AF:

0.0214

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00604

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00216

Gnomad OTH exome

AF:

0.00799

GnomAD4 exome

AF:

0.00373

AC:

5445

AN:

1461080

Hom.:

107

Cov.:

AF XY:

0.00364

AC XY:

2644

AN XY:

726844

show subpopulations

Gnomad4 AFR exome

AF:

0.0577

Gnomad4 AMR exome

AF:

0.00651

Gnomad4 ASJ exome

AF:

0.0231

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00542

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.00121

Gnomad4 OTH exome

AF:

0.00859

GnomAD4 genome

AF:

0.0181

AC:

2764

AN:

152306

Hom.:

Cov.:

AF XY:

0.0179

AC XY:

1330

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0558

Gnomad4 AMR

AF:

0.00791

Gnomad4 ASJ

AF:

0.0219

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00580

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00231

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.00998

Hom.:

Bravo

AF:

0.0207

EpiCase

AF:

0.00420

EpiControl

AF:

0.00326

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 20, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.044

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over