Variant chr22-36937752-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000395.3(CSF2RB):c.1944A>G(p.Pro648Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 1,569,224 control chromosomes in the GnomAD database, including 522,375 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.77 ( 46289 hom., cov: 31)

Exomes 𝑓: 0.82 ( 476086 hom. )

Consequence

CSF2RB
NM_000395.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.270

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=-0.96).

BP6

Variant 22-36937752-A-G is Benign according to our data. Variant chr22-36937752-A-G is described in ClinVar as [Benign]. Clinvar id is 226549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36937752-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSF2RB	NM_000395.3 linkuse as main transcript	c.1944A>G	p.Pro648Pro	synonymous_variant	14/14	ENST00000403662.8	NP_000386.1	P32927-1Q6NSJ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF2RB	ENST00000403662.8 linkuse as main transcript	c.1944A>G	p.Pro648Pro	synonymous_variant	14/14	5	NM_000395.3	ENSP00000384053.3		P32927-1
CSF2RB	ENST00000406230.5 linkuse as main transcript	c.1962A>G	p.Pro654Pro	synonymous_variant	13/13	1		ENSP00000385271.1		P32927-2

Frequencies

GnomAD3 genomes

AF:

0.774

AC:

117655

AN:

151950

Hom.:

46252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.637

Gnomad AMI

AF:

0.751

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.785

Gnomad EAS

AF:

0.939

Gnomad SAS

AF:

0.876

Gnomad FIN

AF:

0.861

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.814

Gnomad OTH

AF:

0.776

GnomAD3 exomes

AF:

0.833

AC:

149507

AN:

179536

Hom.:

62610

AF XY:

0.834

AC XY:

80324

AN XY:

96318

show subpopulations

Gnomad AFR exome

AF:

0.634

Gnomad AMR exome

AF:

0.886

Gnomad ASJ exome

AF:

0.784

Gnomad EAS exome

AF:

0.944

Gnomad SAS exome

AF:

0.866

Gnomad FIN exome

AF:

0.867

Gnomad NFE exome

AF:

0.809

Gnomad OTH exome

AF:

0.817

GnomAD4 exome

AF:

0.818

AC:

1159801

AN:

1417156

Hom.:

476086

Cov.:

AF XY:

0.819

AC XY:

574293

AN XY:

700912

show subpopulations

Gnomad4 AFR exome

AF:

0.625

Gnomad4 AMR exome

AF:

0.879

Gnomad4 ASJ exome

AF:

0.789

Gnomad4 EAS exome

AF:

0.945

Gnomad4 SAS exome

AF:

0.865

Gnomad4 FIN exome

AF:

0.866

Gnomad4 NFE exome

AF:

0.813

Gnomad4 OTH exome

AF:

0.815

GnomAD4 genome

AF:

0.774

AC:

117750

AN:

152068

Hom.:

46289

Cov.:

AF XY:

0.779

AC XY:

57930

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.638

Gnomad4 AMR

AF:

0.822

Gnomad4 ASJ

AF:

0.785

Gnomad4 EAS

AF:

0.940

Gnomad4 SAS

AF:

0.876

Gnomad4 FIN

AF:

0.861

Gnomad4 NFE

AF:

0.814

Gnomad4 OTH

AF:

0.777

Alfa

AF:

0.803

Hom.:

55495

Bravo

AF:

0.767

Asia WGS

AF:

0.866

AC:

3013

AN:

3478

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 28, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 24, 2014

Pro648Pro 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 34.1% (1489/4366) of African American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs131840). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.4

DANN

Benign

0.18

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