rs6000488

chr22-36925818-G-Achr22-36925818-G-T

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.201-169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,124 control chromosomes in the GnomAD database, including 1,221 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1221 hom., cov: 32)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.418

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]

LOC105373023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 22-36925818-G-A is Benign according to our data. Variant chr22-36925818-G-A is described in ClinVar as [Benign]. Clinvar id is 1288350.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RB	NM_000395.3	c.201-169G>A		intron_variant		ENST00000403662.8
LOC105373023	XR_938230.2	n.126C>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RB	ENST00000403662.8	c.201-169G>A		intron_variant		5	NM_000395.3	P1
CSF2RB	ENST00000406230.5	c.201-169G>A		intron_variant		1
CSF2RB	ENST00000421539.1	c.-40-169G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17605 AN: 152006 Hom.: 1221 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0467

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.116 AC: 17621 AN: 152124 Hom.: 1221 Cov.: 32 AF XY: 0.112 AC XY: 8346 AN XY: 74370

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0819

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0467

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.129

Alfa AF: 0.102 Hom.: 786

Bravo AF: 0.119

Asia WGS AF: 0.0730 AC: 254 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

Nov 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.0
Dann	Benign	0.45

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

Other links and lift over

dbSNP: rs6000488; hg19: chr22-37321860;