Variant X-47624449-T-TTAGGGGTGGGGAGGAACGGAAGGGAGAATCTCAGGGAAGGCAAGAATGCATTCAATTCTTATTGAGTGCCTCAGGCCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001145252.3(CFP):c.1245-10_1245-9insGGGCCTGAGGCACTCAATAAGAATTGAATGCATTCTTGCCTTCCCTGAGATTCTCCCTTCCGTTCCTCCCCACCCCTA variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000045 ( 0 hom., 0 hem., cov: 22)

Exomes 𝑓: 0.000016 ( 0 hom. 5 hem. )

Failed GnomAD Quality Control

Consequence

CFP
NM_001145252.3 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.14

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFP	NM_001145252.3 linkuse as main transcript	c.1245-10_1245-9insGGGCCTGAGGCACTCAATAAGAATTGAATGCATTCTTGCCTTCCCTGAGATTCTCCCTTCCGTTCCTCCCCACCCCTA		splice_polypyrimidine_tract_variant, intron_variant		ENST00000396992.8
CFP	NM_002621.2 linkuse as main transcript	c.1245-10_1245-9insGGGCCTGAGGCACTCAATAAGAATTGAATGCATTCTTGCCTTCCCTGAGATTCTCCCTTCCGTTCCTCCCCACCCCTA		splice_polypyrimidine_tract_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
CFP	ENST00000396992.8 linkuse as main transcript	c.1245-10_1245-9insGGGCCTGAGGCACTCAATAAGAATTGAATGCATTCTTGCCTTCCCTGAGATTCTCCCTTCCGTTCCTCCCCACCCCTA	splice_polypyrimidine_tract_variant, intron_variant	1	NM_001145252.3	P1
CFP	ENST00000247153.7 linkuse as main transcript	c.1245-10_1245-9insGGGCCTGAGGCACTCAATAAGAATTGAATGCATTCTTGCCTTCCCTGAGATTCTCCCTTCCGTTCCTCCCCACCCCTA	splice_polypyrimidine_tract_variant, intron_variant	5		P1
CFP	ENST00000478222.1 linkuse as main transcript	n.366-10_366-9insGGGCCTGAGGCACTCAATAAGAATTGAATGCATTCTTGCCTTCCCTGAGATTCTCCCTTCCGTTCCTCCCCACCCCTA	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	2
CFP	ENST00000640573.1 linkuse as main transcript	n.1483-10_1483-9insGGGCCTGAGGCACTCAATAAGAATTGAATGCATTCTTGCCTTCCCTGAGATTCTCCCTTCCGTTCCTCCCCACCCCTA	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

110029

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

32389

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000949

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000156

AC:

AN:

1092386

Hom.:

Cov.:

AF XY:

0.0000140

AC XY:

AN XY:

358106

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000495

Gnomad4 NFE exome

AF:

0.0000179

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000454

AC:

AN:

110029

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

32389

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000949

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Oct 11, 2023

This sequence change falls in intron 9 of the CFP gene. It does not directly change the encoded amino acid sequence of the CFP protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CFP-related conditions. ClinVar contains an entry for this variant (Variation ID: 1411578). Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over