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Y-1282760-C-T

Variant names:

• chrY-1282760-C-T
• rs1399172803
• ENST00000972697.1:c.57C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The ENST00000972697.1(CSF2RA):​c.57C>T​(p.Leu19Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov:)
• Consequence: CSF2RA ENST00000972697.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.295
• Publications: 0 publications found

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]

CSF2RA Gene-Disease associations (from GenCC):

• surfactant metabolism dysfunction, pulmonary, 4

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
• hereditary pulmonary alveolar proteinosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CSF2RA (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.931).
• BP7: Synonymous conserved (PhyloP=-0.295 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000972697.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSF2RA_1	NM_001161530.2_1		c.57C>T	p.Leu19Leu	synonymous	Exon 3 of 14
	CSF2RA_1	NM_001379153.1_1		c.57C>T	p.Leu19Leu	synonymous	Exon 2 of 13
	CSF2RA_1	NM_001379154.1_1		c.57C>T	p.Leu19Leu	synonymous	Exon 3 of 14

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSF2RA	ENST00000972697.1		c.57C>T	p.Leu19Leu	synonymous	Exon 3 of 13	ENSP00000642755.1
	CSF2RA	ENST00000972778.1		c.57C>T	p.Leu19Leu	synonymous	Exon 3 of 14	ENSP00000642789.1
	CSF2RA	ENST00000972964.1		c.57C>T	p.Leu19Leu	synonymous	Exon 3 of 14	ENSP00000642826.1

Frequencies

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

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

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Surfactant metabolism dysfunction, pulmonary, 4 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.93
PhyloP100		-0.29
PromoterAI		-0.014	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1399172803; hg19: chrY-1351653;