22-36921806-T-C

Variant names:

• chr22-36921806-T-C
• rs5756408
• NM_000395.3:c.-172-230T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000395.3(CSF2RB):​c.-172-230T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,746 control chromosomes in the GnomAD database, including 16,889 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.44 (16889 hom., cov: 32)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.03

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]

ENSG00000304449 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 22-36921806-T-C is Benign according to our data. Variant chr22-36921806-T-C is described in ClinVar as [Benign]. Clinvar id is 1271192.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSF2RB	NM_000395.3	c.-172-230T>C		intron_variant	Intron 1 of 13	ENST00000403662.8	NP_000386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSF2RB	ENST00000403662.8	c.-172-230T>C		intron_variant	Intron 1 of 13	5	NM_000395.3	ENSP00000384053.3
ENSG00000304449	ENST00000803517.1	n.232+3944A>G		intron_variant	Intron 1 of 1
ENSG00000304449	ENST00000803518.1	n.275-2867A>G		intron_variant	Intron 1 of 1
ENSG00000304449	ENST00000803519.1	n.261+1493A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67182 AN: 151630 Hom.: 16881 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.443 AC: 67215 AN: 151746 Hom.: 16889 Cov.: 32 AF XY: 0.450 AC XY: 33363 AN XY: 74164

African (AFR) AF: 0.198 AC: 8172 AN: 41188

American (AMR) AF: 0.590 AC: 9025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1787 AN: 3468

East Asian (EAS) AF: 0.599 AC: 3091 AN: 5158

South Asian (SAS) AF: 0.398 AC: 1918 AN: 4824

European-Finnish (FIN) AF: 0.563 AC: 5962 AN: 10582

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35684 AN: 67924

Other (OTH) AF: 0.452 AC: 952 AN: 2108

Alfa AF: 0.331 Hom.: 1135

Bravo AF: 0.434

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.81
DANN	Benign	0.22
PhyloP100		-4.0
PromoterAI		-0.021	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs5756408; hg19: chr22-37317848;