Variant rs16846 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000395.3(CSF2RB):c.702C>T(p.Cys234=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 1,613,734 control chromosomes in the GnomAD database, including 1,309 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 194 hom., cov: 32)

Exomes 𝑓: 0.035 ( 1115 hom. )

Consequence

CSF2RB
NM_000395.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0170

Variant links:

Genes affected

CSF2RB (HGNC:2436): (colony stimulating factor 2 receptor subunit beta) The protein encoded by this gene is the common beta chain of the high affinity receptor for IL-3, IL-5 and CSF. Defects in this gene have been reported to be associated with protein alveolar proteinosis (PAP). [provided by RefSeq, Jul 2008]

CSF2RB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 22-36929791-C-T is Benign according to our data. Variant chr22-36929791-C-T is described in ClinVar as [Benign]. Clinvar id is 226554.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36929791-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RB	NM_000395.3 linkuse as main transcript	c.702C>T	p.Cys234=	synonymous_variant	6/14	ENST00000403662.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RB	ENST00000403662.8 linkuse as main transcript	c.702C>T	p.Cys234=	synonymous_variant	6/14	5	NM_000395.3	P1	P32927-1
CSF2RB	ENST00000406230.5 linkuse as main transcript	c.702C>T	p.Cys234=	synonymous_variant	5/13	1			P32927-2
CSF2RB	ENST00000421539.1 linkuse as main transcript	c.462C>T	p.Cys154=	synonymous_variant	5/7	5

Frequencies

GnomAD3 genomes

AF:

0.0455

AC:

6926

AN:

152188

Hom.:

193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0783

Gnomad AMI

AF:

0.0518

Gnomad AMR

AF:

0.0429

Gnomad ASJ

AF:

0.0256

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0186

Gnomad FIN

AF:

0.0102

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.0371

Gnomad OTH

AF:

0.0578

GnomAD3 exomes

AF:

0.0324

AC:

8058

AN:

248422

Hom.:

176

AF XY:

0.0325

AC XY:

4389

AN XY:

134940

show subpopulations

Gnomad AFR exome

AF:

0.0763

Gnomad AMR exome

AF:

0.0275

Gnomad ASJ exome

AF:

0.0265

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0190

Gnomad FIN exome

AF:

0.00977

Gnomad NFE exome

AF:

0.0407

Gnomad OTH exome

AF:

0.0496

GnomAD4 exome

AF:

0.0347

AC:

50686

AN:

1461428

Hom.:

1115

Cov.:

AF XY:

0.0348

AC XY:

25274

AN XY:

727012

show subpopulations

Gnomad4 AFR exome

AF:

0.0815

Gnomad4 AMR exome

AF:

0.0301

Gnomad4 ASJ exome

AF:

0.0256

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0181

Gnomad4 FIN exome

AF:

0.0107

Gnomad4 NFE exome

AF:

0.0366

Gnomad4 OTH exome

AF:

0.0389

GnomAD4 genome

AF:

0.0455

AC:

6935

AN:

152306

Hom.:

194

Cov.:

AF XY:

0.0441

AC XY:

3283

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0783

Gnomad4 AMR

AF:

0.0428

Gnomad4 ASJ

AF:

0.0256

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0195

Gnomad4 FIN

AF:

0.0102

Gnomad4 NFE

AF:

0.0371

Gnomad4 OTH

AF:

0.0568

Alfa

AF:

0.0432

Hom.:

Bravo

AF:

0.0495

Asia WGS

AF:

0.0200

AC:

AN:

3478

EpiCase

AF:

0.0502

EpiControl

AF:

0.0454

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 25, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 24, 2014

Cys234Cys in exon 6 of CSF2RB: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 8.0% (352/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs16846). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.53

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.53

Position offset: -6

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