X-1282485-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000432318.8(CSF2RA):c.-102G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 635,396 control chromosomes in the GnomAD database, including 547 homozygotes. There are 4,022 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.041 (418 hom., 2879 hem., cov: 31)
  • Exomes 𝑓: 0.0053 (129 hom. 1143 hem.)
• Consequence: CSF2RA ENST00000432318.8 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.42

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP6: Variant X-1282485-G-A is Benign according to our data. Variant chrX-1282485-G-A is described in ClinVar as [Benign]. Clinvar id is 1268410.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RA	NM_172245.4	c.-26-193G>A		intron_variant		ENST00000381529.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RA	ENST00000381529.9	c.-26-193G>A		intron_variant		1	NM_172245.4	A2

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6187 AN: 151908 Hom.: 418 Cov.: 31 AF XY: 0.0387 AC XY: 2870 AN XY: 74160

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0141

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000676

Gnomad OTH AF: 0.0283

GnomAD4 exome AF: 0.00526 AC: 2541 AN: 483370 Hom.: 129 Cov.: 0 AF XY: 0.00445 AC XY: 1143 AN XY: 257032

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.00790

Gnomad4 ASJ exome AF: 0.000471

Gnomad4 EAS exome AF: 0.00127

Gnomad4 SAS exome AF: 0.00138

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000504

Gnomad4 OTH exome AF: 0.00937

GnomAD4 genome AF: 0.0407 AC: 6193 AN: 152026 Hom.: 418 Cov.: 31 AF XY: 0.0388 AC XY: 2879 AN XY: 74288

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0141

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.00208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000676

Gnomad4 OTH AF: 0.0280

Bravo AF: 0.0458

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

Sep 24, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	0.080
Dann	Benign	0.86

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: rs181469243; hg19: chrX-1401378;