chr22-36925038-T-C

Position:

• chr22-36925038-T-C

Variant summary

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

The NM_000395.3(CSF2RB):​c.201-949T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,090 control chromosomes in the GnomAD database, including 14,542 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 0.40 (14542 hom., cov: 32)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSF2RB	NM_000395.3	c.201-949T>C		intron_variant		ENST00000403662.8	NP_000386.1
LOC105373023	XR_938230.2	n.194+712A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSF2RB	ENST00000403662.8	c.201-949T>C		intron_variant		5	NM_000395.3	ENSP00000384053	P1
CSF2RB	ENST00000406230.5	c.201-949T>C		intron_variant		1		ENSP00000385271
CSF2RB	ENST00000421539.1	c.-40-949T>C		intron_variant		5		ENSP00000393585

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60963 AN: 151972 Hom.: 14537 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.401 AC: 60984 AN: 152090 Hom.: 14542 Cov.: 32 AF XY: 0.413 AC XY: 30703 AN XY: 74328

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.392

Alfa AF: 0.370 Hom.: 2118

Bravo AF: 0.389

Asia WGS AF: 0.603 AC: 2094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.34

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: rs2284031; hg19: chr22-37321080;