Variant chr5-150061081-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.1859-109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 730,412 control chromosomes in the GnomAD database, including 113,100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.49 ( 19793 hom., cov: 30)

Exomes 𝑓: 0.56 ( 93307 hom. )

Consequence

CSF1R
NM_001288705.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.923

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=-0.82).

BP6

Variant 5-150061081-C-T is Benign according to our data. Variant chr5-150061081-C-T is described in ClinVar as [Benign]. Clinvar id is 1220882.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 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.1859-109G>A		intron_variant		ENST00000675795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF1R	ENST00000675795.1 linkuse as main transcript	c.1859-109G>A		intron_variant			NM_001288705.3	P1	P07333-1

Frequencies

GnomAD3 genomes

AF:

0.490

AC:

74315

AN:

151748

Hom.:

19796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.506

Gnomad AMR

AF:

0.425

Gnomad ASJ

AF:

0.553

Gnomad EAS

AF:

0.451

Gnomad SAS

AF:

0.516

Gnomad FIN

AF:

0.676

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.600

Gnomad OTH

AF:

0.474

GnomAD4 exome

AF:

0.559

AC:

323371

AN:

578544

Hom.:

93307

AF XY:

0.560

AC XY:

168560

AN XY:

301174

show subpopulations

Gnomad4 AFR exome

AF:

0.279

Gnomad4 AMR exome

AF:

0.417

Gnomad4 ASJ exome

AF:

0.545

Gnomad4 EAS exome

AF:

0.424

Gnomad4 SAS exome

AF:

0.517

Gnomad4 FIN exome

AF:

0.673

Gnomad4 NFE exome

AF:

0.592

Gnomad4 OTH exome

AF:

0.534

GnomAD4 genome

AF:

0.489

AC:

74325

AN:

151868

Hom.:

19793

Cov.:

AF XY:

0.492

AC XY:

36513

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.425

Gnomad4 ASJ

AF:

0.553

Gnomad4 EAS

AF:

0.452

Gnomad4 SAS

AF:

0.517

Gnomad4 FIN

AF:

0.676

Gnomad4 NFE

AF:

0.600

Gnomad4 OTH

AF:

0.471

Alfa

AF:

0.528

Hom.:

7338

Bravo

AF:

0.461

Asia WGS

AF:

0.432

AC:

1500

AN:

3476

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

-0.82

CADD

Benign

1.6

DANN

Benign

0.57

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