rs1801116

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_000395.3(CSF2RB):c.2400G>A(p.Pro800=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0279 in 1,614,078 control chromosomes in the GnomAD database, including 710 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 44 hom., cov: 32)

Exomes 𝑓: 0.028 ( 666 hom. )

Consequence

CSF2RB
NM_000395.3 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.287

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 22-36938208-G-A is Benign according to our data. Variant chr22-36938208-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 226552.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.287 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0231 (3514/152224) while in subpopulation NFE AF= 0.0282 (1917/67990). AF 95% confidence interval is 0.0271. There are 44 homozygotes in gnomad4. There are 1683 alleles in male gnomad4 subpopulation. This position pass quality control queck.

BS2

High Homozygotes in GnomAd at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RB	NM_000395.3 linkuse as main transcript	c.2400G>A	p.Pro800=	synonymous_variant	14/14	ENST00000403662.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RB	ENST00000403662.8 linkuse as main transcript	c.2400G>A	p.Pro800=	synonymous_variant	14/14	5	NM_000395.3	P1	P32927-1
CSF2RB	ENST00000406230.5 linkuse as main transcript	c.2418G>A	p.Pro806=	synonymous_variant	13/13	1			P32927-2

Frequencies

GnomAD3 genomes

AF:

0.0231

AC:

3512

AN:

152106

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0164

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.0202

Gnomad ASJ

AF:

0.0337

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.0230

Gnomad FIN

AF:

0.0245

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0282

Gnomad OTH

AF:

0.0263

GnomAD3 exomes

AF:

0.0229

AC:

5758

AN:

251372

Hom.:

AF XY:

0.0236

AC XY:

3201

AN XY:

135864

show subpopulations

Gnomad AFR exome

AF:

0.0169

Gnomad AMR exome

AF:

0.0113

Gnomad ASJ exome

AF:

0.0309

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0219

Gnomad FIN exome

AF:

0.0272

Gnomad NFE exome

AF:

0.0294

Gnomad OTH exome

AF:

0.0299

GnomAD4 exome

AF:

0.0284

AC:

41549

AN:

1461854

Hom.:

666

Cov.:

AF XY:

0.0284

AC XY:

20685

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.0162

Gnomad4 AMR exome

AF:

0.0111

Gnomad4 ASJ exome

AF:

0.0332

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0230

Gnomad4 FIN exome

AF:

0.0280

Gnomad4 NFE exome

AF:

0.0308

Gnomad4 OTH exome

AF:

0.0260

GnomAD4 genome

AF:

0.0231

AC:

3514

AN:

152224

Hom.:

Cov.:

AF XY:

0.0226

AC XY:

1683

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0164

Gnomad4 AMR

AF:

0.0202

Gnomad4 ASJ

AF:

0.0337

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.0232

Gnomad4 FIN

AF:

0.0245

Gnomad4 NFE

AF:

0.0282

Gnomad4 OTH

AF:

0.0260

Alfa

AF:

0.0275

Hom.:

Bravo

AF:

0.0220

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.0293

EpiControl

AF:

0.0291

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2020	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 24, 2014

Pro800Pro in exon 14 of CSF2RB: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue and is not located wi thin the splice consensus sequence. It has been identified in 2.8% (245/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS; dbSNP rs1801116). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

Cadd

Benign

5.5

Dann

Benign

0.40

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