22-36922384-C-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.76+101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 1,118,476 control chromosomes in the GnomAD database, including 146,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (16318 hom., cov: 32)
  • Exomes 𝑓: 0.51 (130329 hom.)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.44

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=-0.82).
• BP6: Variant 22-36922384-C-T is Benign according to our data. Variant chr22-36922384-C-T is described in ClinVar as [Benign]. Clinvar id is 1225537.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RB	NM_000395.3	c.76+101C>T		intron_variant		ENST00000403662.8
LOC105373023	XR_938230.2	n.194+3366G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RB	ENST00000403662.8	c.76+101C>T		intron_variant		5	NM_000395.3	P1
CSF2RB	ENST00000406230.5	c.76+101C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66117 AN: 151740 Hom.: 16309 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.446

GnomAD4 exome AF: 0.513 AC: 496202 AN: 966618 Hom.: 130329 AF XY: 0.510 AC XY: 249672 AN XY: 489130

Gnomad4 AFR exome AF: 0.185

Gnomad4 AMR exome AF: 0.653

Gnomad4 ASJ exome AF: 0.502

Gnomad4 EAS exome AF: 0.608

Gnomad4 SAS exome AF: 0.409

Gnomad4 FIN exome AF: 0.569

Gnomad4 NFE exome AF: 0.521

Gnomad4 OTH exome AF: 0.501

GnomAD4 genome AF: 0.436 AC: 66151 AN: 151858 Hom.: 16318 Cov.: 32 AF XY: 0.442 AC XY: 32773 AN XY: 74206

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.448

Alfa AF: 0.491 Hom.: 3816

Bravo AF: 0.429

Asia WGS AF: 0.495 AC: 1720 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 10, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.47
Dann	Benign	0.71

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: rs2280976; hg19: chr22-37318426; COSMIC: COSV53259868; COSMIC: COSV53259868;