Variant rs3829987 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001288705.3(CSF1R):c.889+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,613,674 control chromosomes in the GnomAD database, including 8,484 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 3060 hom., cov: 32)

Exomes 𝑓: 0.051 ( 5424 hom. )

Consequence

CSF1R
NM_001288705.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.02

Variant links:

Genes affected

CSF1R (HGNC:2433): (colony stimulating factor 1 receptor) The protein encoded by this gene is the receptor for colony stimulating factor 1, a cytokine which controls the production, differentiation, and function of macrophages. This receptor mediates most if not all of the biological effects of this cytokine. Ligand binding activates the receptor kinase through a process of oligomerization and transphosphorylation. The encoded protein is a tyrosine kinase transmembrane receptor and member of the CSF1/PDGF receptor family of tyrosine-protein kinases. Mutations in this gene have been associated with a predisposition to myeloid malignancy. The first intron of this gene contains a transcriptionally inactive ribosomal protein L7 processed pseudogene oriented in the opposite direction. Alternative splicing results in multiple transcript variants. Expression of a splice variant from an LTR promoter has been found in Hodgkin lymphoma (HL), HL cell lines and anaplastic large cell lymphoma. [provided by RefSeq, Mar 2017]

CSF1R links:

CSF1R (HGNC:):

CSF1R links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 5-150077248-G-A is Benign according to our data. Variant chr5-150077248-G-A is described in ClinVar as [Benign]. Clinvar id is 1239548.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSF1R	NM_001288705.3 linkuse as main transcript	c.889+28C>T		intron_variant		ENST00000675795.1	NP_001275634.1	P07333-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF1R	ENST00000675795.1 linkuse as main transcript	c.889+28C>T		intron_variant			NM_001288705.3	ENSP00000501699.1		P07333-1

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21764

AN:

152010

Hom.:

3047

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.0533

Gnomad FIN

AF:

0.0478

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0299

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.101

AC:

25309

AN:

251444

Hom.:

2763

AF XY:

0.0861

AC XY:

11696

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.350

Gnomad AMR exome

AF:

0.248

Gnomad ASJ exome

AF:

0.0525

Gnomad EAS exome

AF:

0.226

Gnomad SAS exome

AF:

0.0447

Gnomad FIN exome

AF:

0.0502

Gnomad NFE exome

AF:

0.0302

Gnomad OTH exome

AF:

0.0757

GnomAD4 exome

AF:

0.0513

AC:

75025

AN:

1461546

Hom.:

5424

Cov.:

AF XY:

0.0494

AC XY:

35942

AN XY:

727096

show subpopulations

Gnomad4 AFR exome

AF:

0.357

Gnomad4 AMR exome

AF:

0.240

Gnomad4 ASJ exome

AF:

0.0497

Gnomad4 EAS exome

AF:

0.208

Gnomad4 SAS exome

AF:

0.0449

Gnomad4 FIN exome

AF:

0.0492

Gnomad4 NFE exome

AF:

0.0280

Gnomad4 OTH exome

AF:

0.0758

GnomAD4 genome

AF:

0.143

AC:

21824

AN:

152128

Hom.:

3060

Cov.:

AF XY:

0.144

AC XY:

10696

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.345

Gnomad4 AMR

AF:

0.198

Gnomad4 ASJ

AF:

0.0510

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.0533

Gnomad4 FIN

AF:

0.0478

Gnomad4 NFE

AF:

0.0299

Gnomad4 OTH

AF:

0.147

Alfa

AF:

0.0612

Hom.:

787

Bravo

AF:

0.166

Asia WGS

AF:

0.172

AC:

600

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.070

DANN

Benign

0.45

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