Variant 22-36933957-C-T 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.1278C>T(p.Ser426=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,612,486 control chromosomes in the GnomAD database, including 39,782 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3444 hom., cov: 31)

Exomes 𝑓: 0.22 ( 36338 hom. )

Consequence

CSF2RB
NM_000395.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.990

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 22-36933957-C-T is Benign according to our data. Variant chr22-36933957-C-T is described in ClinVar as [Benign]. Clinvar id is 226545.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-36933957-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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.1278C>T	p.Ser426=	synonymous_variant	10/14	ENST00000403662.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RB	ENST00000403662.8 linkuse as main transcript	c.1278C>T	p.Ser426=	synonymous_variant	10/14	5	NM_000395.3	P1	P32927-1
CSF2RB	ENST00000406230.5 linkuse as main transcript	c.1296C>T	p.Ser432=	synonymous_variant	9/13	1			P32927-2

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31404

AN:

151816

Hom.:

3444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.235

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.0673

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.224

Gnomad OTH

AF:

0.218

GnomAD3 exomes

AF:

0.189

AC:

47091

AN:

249068

Hom.:

5078

AF XY:

0.195

AC XY:

26277

AN XY:

134914

show subpopulations

Gnomad AFR exome

AF:

0.238

Gnomad AMR exome

AF:

0.108

Gnomad ASJ exome

AF:

0.186

Gnomad EAS exome

AF:

0.0615

Gnomad SAS exome

AF:

0.233

Gnomad FIN exome

AF:

0.146

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.195

GnomAD4 exome

AF:

0.218

AC:

318672

AN:

1460552

Hom.:

36338

Cov.:

AF XY:

0.219

AC XY:

159139

AN XY:

726608

show subpopulations

Gnomad4 AFR exome

AF:

0.235

Gnomad4 AMR exome

AF:

0.113

Gnomad4 ASJ exome

AF:

0.191

Gnomad4 EAS exome

AF:

0.0488

Gnomad4 SAS exome

AF:

0.236

Gnomad4 FIN exome

AF:

0.151

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.224

GnomAD4 genome

AF:

0.207

AC:

31407

AN:

151934

Hom.:

3444

Cov.:

AF XY:

0.199

AC XY:

14796

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.235

Gnomad4 AMR

AF:

0.151

Gnomad4 ASJ

AF:

0.179

Gnomad4 EAS

AF:

0.0671

Gnomad4 SAS

AF:

0.208

Gnomad4 FIN

AF:

0.138

Gnomad4 NFE

AF:

0.224

Gnomad4 OTH

AF:

0.215

Alfa

AF:

0.212

Hom.:

2013

Bravo

AF:

0.209

Asia WGS

AF:

0.125

AC:

439

AN:

3478

EpiCase

AF:

0.227

EpiControl

AF:

0.227

ClinVar

Significance: 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	GeneDx	Feb 21, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 24, 2014

Ser426Ser in exon 10 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 23.6% (1042/4406) of African American chromosomes from a broad population by the NHLBI Exome Seque ncing Project (http://evs.gs.washington.edu/EVS; dbSNP rs1801117). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

Cadd

Benign

4.5

Dann

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.26

Position offset: 37

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