chrX-1285484-G-A

Variant names:

• chrX-1285484-G-A
• rs182764964
• NM_172245.4:c.77-294G>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.77-294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,162 control chromosomes in the GnomAD database, including 3,255 homozygotes. There are 13,940 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3255 hom., 13940 hem., cov: 28)
• Consequence: CSF2RA NM_172245.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.614

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=-0.93).
• BP6: Variant X-1285484-G-A is Benign according to our data. Variant chrX-1285484-G-A is described in ClinVar as [Benign]. Clinvar id is 1235660.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSF2RA	NM_172245.4	c.77-294G>A		intron_variant	Intron 3 of 12	ENST00000381529.9	NP_758448.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSF2RA	ENST00000381529.9	c.77-294G>A		intron_variant	Intron 3 of 12	1	NM_172245.4	ENSP00000370940.3

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28532 AN: 151042 Hom.: 3254 Cov.: 28 AF XY: 0.189 AC XY: 13941 AN XY: 73676

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.189 AC: 28532 AN: 151162 Hom.: 3255 Cov.: 28 AF XY: 0.189 AC XY: 13940 AN XY: 73806

Gnomad4 AFR AF: 0.0579

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.213

Bravo AF: 0.178

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 31, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs182764964; hg19: chrX-1404377;