X-1282599-A-AT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_172245.4(CSF2RA):c.-26-78dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,058,094 control chromosomes in the GnomAD database, including 6,331 homozygotes. There are 54,875 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.085 (750 hom., 6436 hem., cov: 29)
  • Exomes 𝑓: 0.10 (5581 hom. 48439 hem.)
• Consequence: CSF2RA NM_172245.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.43

Genes affected

CSF2RA (HGNC:2435): (colony stimulating factor 2 receptor subunit alpha) The protein encoded by this gene is the alpha subunit of the heterodimeric receptor for colony stimulating factor 2, a cytokine which controls the production, differentiation, and function of granulocytes and macrophages. The encoded protein is a member of the cytokine family of receptors. This gene is found in the pseudoautosomal region (PAR) of the X and Y chromosomes. Multiple transcript variants encoding different isoforms have been found for this gene, with some of the isoforms being membrane-bound and others being soluble. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant X-1282599-A-AT is Benign according to our data. Variant chrX-1282599-A-AT is described in ClinVar as [Benign]. Clinvar id is 1280131.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RA	NM_172245.4	c.-26-78dup		intron_variant		ENST00000381529.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RA	ENST00000381529.9	c.-26-78dup		intron_variant		1	NM_172245.4	A2

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12885 AN: 151852 Hom.: 751 Cov.: 29 AF XY: 0.0868 AC XY: 6435 AN XY: 74118

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.0255

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.104 AC: 94677 AN: 906124 Hom.: 5581 Cov.: 13 AF XY: 0.103 AC XY: 48439 AN XY: 471280

Gnomad4 AFR exome AF: 0.0204

Gnomad4 AMR exome AF: 0.192

Gnomad4 ASJ exome AF: 0.0709

Gnomad4 EAS exome AF: 0.0404

Gnomad4 SAS exome AF: 0.0775

Gnomad4 FIN exome AF: 0.149

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.0932

GnomAD4 genome AF: 0.0848 AC: 12880 AN: 151970 Hom.: 750 Cov.: 29 AF XY: 0.0867 AC XY: 6436 AN XY: 74246

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0730

Gnomad4 EAS AF: 0.0250

Gnomad4 SAS AF: 0.0732

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0715

Bravo AF: 0.0808

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

Mar 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs201182273; hg19: chrX-1401492;