Variant 5-150053837-G-GC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001288705.3(CSF1R):c.*231_*232insG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.52 ( 21046 hom., cov: 0)

Exomes 𝑓: 0.58 ( 74156 hom. )

Consequence

CSF1R
NM_001288705.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.788

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-150053837-G-GC is Benign according to our data. Variant chr5-150053837-G-GC is described in ClinVar as [Benign]. Clinvar id is 352114.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF1R	NM_001288705.3 linkuse as main transcript	c.231_232insG		3_prime_UTR_variant	21/21	ENST00000675795.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF1R	ENST00000675795.1 linkuse as main transcript	c.231_232insG	3_prime_UTR_variant	21/21		NM_001288705.3	P1	P07333-1
CSF1R	ENST00000286301.7 linkuse as main transcript	c.231_232insG	3_prime_UTR_variant	22/22	1		P1	P07333-1
CSF1R	ENST00000504875.5 linkuse as main transcript	c.971_972insG	3_prime_UTR_variant, NMD_transcript_variant	20/20	1
CSF1R	ENST00000509861.1 linkuse as main transcript		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.516

AC:

76909

AN:

149072

Hom.:

21046

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.475

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.483

Gnomad SAS

AF:

0.562

Gnomad FIN

AF:

0.685

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.578

AC:

250375

AN:

433266

Hom.:

74156

Cov.:

AF XY:

0.579

AC XY:

131987

AN XY:

227850

show subpopulations

Gnomad4 AFR exome

AF:

0.301

Gnomad4 AMR exome

AF:

0.428

Gnomad4 ASJ exome

AF:

0.610

Gnomad4 EAS exome

AF:

0.445

Gnomad4 SAS exome

AF:

0.566

Gnomad4 FIN exome

AF:

0.676

Gnomad4 NFE exome

AF:

0.608

Gnomad4 OTH exome

AF:

0.558

GnomAD4 genome

AF:

0.516

AC:

76933

AN:

149186

Hom.:

21046

Cov.:

AF XY:

0.517

AC XY:

37730

AN XY:

72940

show subpopulations

Gnomad4 AFR

AF:

0.323

Gnomad4 AMR

AF:

0.440

Gnomad4 ASJ

AF:

0.618

Gnomad4 EAS

AF:

0.484

Gnomad4 SAS

AF:

0.563

Gnomad4 FIN

AF:

0.685

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.490

Alfa

AF:

0.421

Hom.:

1112

Bravo

AF:

0.473

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hereditary diffuse leukoencephalopathy with spheroids

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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