X-1285574-C-A

Position:

• chrX-1285574-C-A

Variant summary

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

The NM_172245.4(CSF2RA):​c.77-204C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 652,624 control chromosomes in the GnomAD database, including 51,329 homozygotes. There are 130,850 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.41 (13331 hom., 30703 hem., cov: 26)
  • Exomes 𝑓: 0.38 (37998 hom. 100147 hem.)
• Consequence: CSF2RA NM_172245.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -5.28

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=-0.98).
• BP6: Variant X-1285574-C-A is Benign according to our data. Variant chrX-1285574-C-A is described in ClinVar as [Benign]. Clinvar id is 1271198.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RA	NM_172245.4	c.77-204C>A		intron_variant		ENST00000381529.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RA	ENST00000381529.9	c.77-204C>A		intron_variant		1	NM_172245.4	A2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 61896 AN: 149988 Hom.: 13305 Cov.: 26 AF XY: 0.420 AC XY: 30641 AN XY: 73002

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.380 AC: 191054 AN: 502526 Hom.: 37998 AF XY: 0.378 AC XY: 100147 AN XY: 264926

Gnomad4 AFR exome AF: 0.489

Gnomad4 AMR exome AF: 0.472

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.509

Gnomad4 SAS exome AF: 0.389

Gnomad4 FIN exome AF: 0.466

Gnomad4 NFE exome AF: 0.356

Gnomad4 OTH exome AF: 0.374

GnomAD4 genome AF: 0.413 AC: 61961 AN: 150098 Hom.: 13331 Cov.: 26 AF XY: 0.420 AC XY: 30703 AN XY: 73124

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.340

Bravo AF: 0.414

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

Dec 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0010
DANN	Benign	0.31

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: rs28427040; hg19: chrX-1404467;