Variant chr5-150080011-C-T 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.592+41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 1,591,254 control chromosomes in the GnomAD database, including 12,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1130 hom., cov: 33)

Exomes 𝑓: 0.12 ( 11460 hom. )

Consequence

CSF1R
NM_001288705.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.29

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 -14 ACMG points.

BP4

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

BP6

Variant 5-150080011-C-T is Benign according to our data. Variant chr5-150080011-C-T is described in ClinVar as [Benign]. Clinvar id is 1253351.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 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.592+41G>A		intron_variant		ENST00000675795.1	NP_001275634.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF1R	ENST00000675795.1 linkuse as main transcript	c.592+41G>A		intron_variant			NM_001288705.3	ENSP00000501699	P1	P07333-1

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18352

AN:

152140

Hom.:

1130

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.131

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.0706

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.124

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.120

AC:

28481

AN:

237290

Hom.:

1753

AF XY:

0.120

AC XY:

15367

AN XY:

127632

show subpopulations

Gnomad AFR exome

AF:

0.121

Gnomad AMR exome

AF:

0.117

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.140

Gnomad SAS exome

AF:

0.131

Gnomad FIN exome

AF:

0.0748

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.124

AC:

178210

AN:

1438998

Hom.:

11460

Cov.:

AF XY:

0.124

AC XY:

88090

AN XY:

712218

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.141

Gnomad4 EAS exome

AF:

0.120

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.0805

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.136

GnomAD4 genome

AF:

0.121

AC:

18356

AN:

152256

Hom.:

1130

Cov.:

AF XY:

0.120

AC XY:

8901

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.119

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.136

Gnomad4 EAS

AF:

0.139

Gnomad4 SAS

AF:

0.127

Gnomad4 FIN

AF:

0.0706

Gnomad4 NFE

AF:

0.124

Gnomad4 OTH

AF:

0.129

Alfa

AF:

0.124

Hom.:

814

Bravo

AF:

0.125

Asia WGS

AF:

0.152

AC:

526

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

-0.90

CADD

Benign

0.0070

DANN

Benign

0.75

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