rs8177079

Positions:

• chrX-47625846-G-A
• chrX-47625846-G-C
• chrX-47625846-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001145252.3(CFP):​c.1244+212C>T variant causes a intron 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: 𝑓 0.78 (23746 hom., 25077 hem., cov: 22)
  • Exomes 𝑓: 0.77 (68502 hom. 90453 hem.)
  • Failed GnomAD Quality Control
• Consequence: CFP NM_001145252.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

CFP (HGNC:8864): (complement factor properdin) This gene encodes a plasma glycoprotein that positively regulates the alternative complement pathway of the innate immune system. This protein binds to many microbial surfaces and apoptotic cells and stabilizes the C3- and C5-convertase enzyme complexes in a feedback loop that ultimately leads to formation of the membrane attack complex and lysis of the target cell. Mutations in this gene result in two forms of properdin deficiency, which results in high susceptibility to meningococcal infections. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Feb 2009]

CFP (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFP	NM_001145252.3	c.1244+212C>T		intron_variant		ENST00000396992.8	NP_001138724.1
CFP	NM_002621.2	c.1244+212C>T		intron_variant			NP_002612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFP	ENST00000396992.8	c.1244+212C>T		intron_variant		1	NM_001145252.3	ENSP00000380189.3

Frequencies

GnomAD3 genomes AF: 0.779 AC: 85591 AN: 109934 Hom.: 23749 Cov.: 22 AF XY: 0.777 AC XY: 25020 AN XY: 32204

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.781

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.772 AC: 266343 AN: 345106 Hom.: 68502 Cov.: 3 AF XY: 0.770 AC XY: 90453 AN XY: 117542

Gnomad4 AFR exome AF: 0.824

Gnomad4 AMR exome AF: 0.752

Gnomad4 ASJ exome AF: 0.837

Gnomad4 EAS exome AF: 0.984

Gnomad4 SAS exome AF: 0.735

Gnomad4 FIN exome AF: 0.785

Gnomad4 NFE exome AF: 0.747

Gnomad4 OTH exome AF: 0.775

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.779 AC: 85637 AN: 109989 Hom.: 23746 Cov.: 22 AF XY: 0.777 AC XY: 25077 AN XY: 32269

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.781

Alfa AF: 0.753 Hom.: 40737

Bravo AF: 0.782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.78

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: rs8177079; hg19: chrX-47485245;