Variant 22-36921991-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_000395.3(CSF2RB):c.-172-45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0389 in 598,760 control chromosomes in the GnomAD database, including 598 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.032 ( 119 hom., cov: 33)

Exomes 𝑓: 0.041 ( 479 hom. )

Consequence

CSF2RB
NM_000395.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.10

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:

LOC105373023 (HGNC:):

LOC105373023 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=-0.9).

BP6

Variant 22-36921991-C-T is Benign according to our data. Variant chr22-36921991-C-T is described in ClinVar as [Benign]. Clinvar id is 1283425.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0318 (4841/152292) while in subpopulation NFE AF= 0.0484 (3292/68008). AF 95% confidence interval is 0.047. There are 119 homozygotes in gnomad4. There are 2289 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 119 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSF2RB	NM_000395.3 link	c.-172-45C>T		intron_variant		ENST00000403662.8	NP_000386.1	P32927-1Q6NSJ8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF2RB	ENST00000403662.8 link	c.-172-45C>T		intron_variant		5	NM_000395.3	ENSP00000384053.3		P32927-1

Frequencies

GnomAD3 genomes

AF:

0.0318

AC:

4844

AN:

152174

Hom.:

119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00874

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.0215

Gnomad ASJ

AF:

0.0291

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0404

Gnomad FIN

AF:

0.0338

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0484

Gnomad OTH

AF:

0.0387

GnomAD4 exome

AF:

0.0413

AC:

18461

AN:

446468

Hom.:

479

Cov.:

AF XY:

0.0421

AC XY:

9868

AN XY:

234246

show subpopulations

Gnomad4 AFR exome

AF:

0.00800

Gnomad4 AMR exome

AF:

0.0230

Gnomad4 ASJ exome

AF:

0.0276

Gnomad4 EAS exome

AF:

0.000130

Gnomad4 SAS exome

AF:

0.0478

Gnomad4 FIN exome

AF:

0.0348

Gnomad4 NFE exome

AF:

0.0496

Gnomad4 OTH exome

AF:

0.0392

GnomAD4 genome

AF:

0.0318

AC:

4841

AN:

152292

Hom.:

119

Cov.:

AF XY:

0.0307

AC XY:

2289

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.00871

Gnomad4 AMR

AF:

0.0214

Gnomad4 ASJ

AF:

0.0291

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0404

Gnomad4 FIN

AF:

0.0338

Gnomad4 NFE

AF:

0.0484

Gnomad4 OTH

AF:

0.0383

Alfa

AF:

0.0464

Hom.:

Bravo

AF:

0.0301

Asia WGS

AF:

0.0140

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 27, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.42

DANN

Benign

0.54

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