chr4-109792808-A-G

Position:

• chr4-109792808-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000204.5(CFI):​c.57+9107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 151,750 control chromosomes in the GnomAD database, including 4,852 homozygotes. 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 0.18 (4852 hom., cov: 32)
• Consequence: CFI NM_000204.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

CFI (HGNC:5394): (complement factor I) This gene encodes a serine proteinase that is essential for regulating the complement cascade. The encoded preproprotein is cleaved to produce both heavy and light chains, which are linked by disulfide bonds to form a heterodimeric glycoprotein. This heterodimer can cleave and inactivate the complement components C4b and C3b, and it prevents the assembly of the C3 and C5 convertase enzymes. Defects in this gene cause complement factor I deficiency, an autosomal recessive disease associated with a susceptibility to pyogenic infections. Mutations in this gene have been associated with a predisposition to atypical hemolytic uremic syndrome, a disease characterized by acute renal failure, microangiopathic hemolytic anemia and thrombocytopenia. Primary glomerulonephritis with immune deposits and age-related macular degeneration are other conditions associated with mutations of this gene. [provided by RefSeq, Dec 2015]

ENSG00000285330 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFI	NM_000204.5	c.57+9107T>C		intron_variant		ENST00000394634.7	NP_000195.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFI	ENST00000394634.7	c.57+9107T>C		intron_variant		1	NM_000204.5	ENSP00000378130.2
ENSG00000285330	ENST00000645635.1	c.57+9107T>C		intron_variant				ENSP00000493607.1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27663 AN: 151634 Hom.: 4837 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0379

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.183 AC: 27731 AN: 151750 Hom.: 4852 Cov.: 32 AF XY: 0.186 AC XY: 13797 AN XY: 74160

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.0883

Gnomad4 NFE AF: 0.0379

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0612 Hom.: 810

Bravo AF: 0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.54

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: rs10029485; hg19: chr4-110713964;