rs11705394

chr22-36933634-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000395.3(CSF2RB):c.1153-198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,096 control chromosomes in the GnomAD database, including 5,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.25 (5086 hom., cov: 32)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.534

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 22-36933634-T-C is Benign according to our data. Variant chr22-36933634-T-C is described in ClinVar as [Benign]. Clinvar id is 1276886.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RB	NM_000395.3	c.1153-198T>C		intron_variant		ENST00000403662.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RB	ENST00000403662.8	c.1153-198T>C		intron_variant		5	NM_000395.3	P1
CSF2RB	ENST00000406230.5	c.1171-198T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38076 AN: 151978 Hom.: 5087 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0683

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.250 AC: 38087 AN: 152096 Hom.: 5086 Cov.: 32 AF XY: 0.242 AC XY: 17978 AN XY: 74360

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0680

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.258

Alfa AF: 0.252 Hom.: 5430

Bravo AF: 0.255

Asia WGS AF: 0.137 AC: 481 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.042
Dann	Benign	0.17

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: rs11705394; hg19: chr22-37329676;