Variant rs16997510 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000395.3(CSF2RB):c.1569-13T>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0353 in 1,611,906 control chromosomes in the GnomAD database, including 2,083 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.063 ( 577 hom., cov: 31)

Exomes 𝑓: 0.032 ( 1506 hom. )

Consequence

CSF2RB
NM_000395.3 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.86

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 22-36937364-T-G is Benign according to our data. Variant chr22-36937364-T-G is described in ClinVar as [Benign]. Clinvar id is 226547.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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.1569-13T>G		splice_polypyrimidine_tract_variant, intron_variant		ENST00000403662.8	NP_000386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF2RB	ENST00000403662.8 linkuse as main transcript	c.1569-13T>G		splice_polypyrimidine_tract_variant, intron_variant		5	NM_000395.3	ENSP00000384053	P1	P32927-1
CSF2RB	ENST00000406230.5 linkuse as main transcript	c.1587-13T>G		splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000385271		P32927-2

Frequencies

GnomAD3 genomes

AF:

0.0633

AC:

9590

AN:

151432

Hom.:

569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.0560

Gnomad AMR

AF:

0.0369

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.00526

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.0104

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0239

Gnomad OTH

AF:

0.0602

GnomAD3 exomes

AF:

0.0418

AC:

10385

AN:

248670

Hom.:

476

AF XY:

0.0429

AC XY:

5774

AN XY:

134650

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.0253

Gnomad ASJ exome

AF:

0.0326

Gnomad EAS exome

AF:

0.00723

Gnomad SAS exome

AF:

0.104

Gnomad FIN exome

AF:

0.0105

Gnomad NFE exome

AF:

0.0250

Gnomad OTH exome

AF:

0.0397

GnomAD4 exome

AF:

0.0323

AC:

47223

AN:

1460356

Hom.:

1506

Cov.:

AF XY:

0.0341

AC XY:

24762

AN XY:

726568

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

0.0267

Gnomad4 ASJ exome

AF:

0.0316

Gnomad4 EAS exome

AF:

0.00786

Gnomad4 SAS exome

AF:

0.102

Gnomad4 FIN exome

AF:

0.0119

Gnomad4 NFE exome

AF:

0.0244

Gnomad4 OTH exome

AF:

0.0392

GnomAD4 genome

AF:

0.0635

AC:

9622

AN:

151550

Hom.:

577

Cov.:

AF XY:

0.0624

AC XY:

4618

AN XY:

74044

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.0368

Gnomad4 ASJ

AF:

0.0297

Gnomad4 EAS

AF:

0.00527

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0104

Gnomad4 NFE

AF:

0.0239

Gnomad4 OTH

AF:

0.0596

Alfa

AF:

0.0399

Hom.:

Bravo

AF:

0.0681

Asia WGS

AF:

0.0510

AC:

176

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	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 31, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Nov 24, 2014

1569-13T>G in intron 13 of CSF2RB: This variant is not expected to have clinical significance because it has been identified in 15.7% (690/4406) of African Amer ican chromosomes from a broad population by the NHLBI Exome Sequencing Project ( http://evs.gs.washington.edu/EVS; dbSNP rs16997510). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.055

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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