chr22-36923039-T-G

Position:

• chr22-36923039-T-G

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.77-205T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,032 control chromosomes in the GnomAD database, including 34,550 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.67 (34550 hom., cov: 31)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.06

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=-0.99).
• BP6: Variant 22-36923039-T-G is Benign according to our data. Variant chr22-36923039-T-G is described in ClinVar as [Benign]. Clinvar id is 1264734.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSF2RB	NM_000395.3	c.77-205T>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.77-205T>G		intron_variant		5	NM_000395.3	ENSP00000384053.3
CSF2RB	ENST00000406230.5	c.77-205T>G		intron_variant		1		ENSP00000385271.1
CSF2RB	ENST00000421539.1	c.-164-205T>G		intron_variant		5		ENSP00000393585.1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101936 AN: 151914 Hom.: 34518 Cov.: 31

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.671 AC: 102029 AN: 152032 Hom.: 34550 Cov.: 31 AF XY: 0.677 AC XY: 50303 AN XY: 74300

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.660

Alfa AF: 0.655 Hom.: 28740

Bravo AF: 0.675

Asia WGS AF: 0.773 AC: 2688 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 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.40
DANN	Benign	0.42

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: rs2072707; hg19: chr22-37319081;