rs17811365

Positions:

• chr22-36926778-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000395.3(CSF2RB):​c.391+601T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 152,230 control chromosomes in the GnomAD database, including 709 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.094 (709 hom., cov: 33)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSF2RB	NM_000395.3	c.391+601T>G		intron_variant		ENST00000403662.8	NP_000386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF2RB	ENST00000403662.8	c.391+601T>G		intron_variant		5	NM_000395.3	ENSP00000384053.3
CSF2RB	ENST00000406230.5	c.391+601T>G		intron_variant		1		ENSP00000385271.1
CSF2RB	ENST00000421539.1	c.151+601T>G		intron_variant		5		ENSP00000393585.1

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14358 AN: 152112 Hom.: 709 Cov.: 33

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0689

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.0867

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0944 AC: 14367 AN: 152230 Hom.: 709 Cov.: 33 AF XY: 0.0955 AC XY: 7111 AN XY: 74432

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.0815

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0689

Gnomad4 NFE AF: 0.0917

Gnomad4 OTH AF: 0.0886

Alfa AF: 0.0962 Hom.: 923

Bravo AF: 0.0936

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.041
DANN	Benign	0.71

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

Other links and lift over

dbSNP: rs17811365; hg19: chr22-37322820;