19-861593-C-G

Variant summary

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

The NM_001928.4(CFD):c.358-106C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 1,376,048 control chromosomes in the GnomAD database, including 234,286 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 0.50 (19661 hom., cov: 20)
  • Exomes 𝑓: 0.58 (214625 hom.)
• Consequence: CFD NM_001928.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

CFD (HGNC:2771): (complement factor D) This gene encodes a member of the S1, or chymotrypsin, family of serine peptidases. This protease catalyzes the cleavage of factor B, the rate-limiting step of the alternative pathway of complement activation. This protein also functions as an adipokine, a cell signaling protein secreted by adipocytes, which regulates insulin secretion in mice. Mutations in this gene underlie complement factor D deficiency, which is associated with recurrent bacterial meningitis infections in human patients. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature protease. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFD	NM_001928.4	c.358-106C>G		intron_variant		ENST00000327726.11
CFD	NM_001317335.2	c.379-106C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFD	ENST00000327726.11	c.358-106C>G		intron_variant		1	NM_001928.4	P2

Frequencies

GnomAD3 genomes AF: 0.501 AC: 73261 AN: 146136 Hom.: 19663 Cov.: 20

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.584 AC: 717651 AN: 1229804 Hom.: 214625 AF XY: 0.584 AC XY: 355743 AN XY: 609578

Gnomad4 AFR exome AF: 0.327

Gnomad4 AMR exome AF: 0.446

Gnomad4 ASJ exome AF: 0.579

Gnomad4 EAS exome AF: 0.289

Gnomad4 SAS exome AF: 0.571

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.607

Gnomad4 OTH exome AF: 0.561

GnomAD4 genome AF: 0.501 AC: 73258 AN: 146244 Hom.: 19661 Cov.: 20 AF XY: 0.500 AC XY: 35550 AN XY: 71060

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.485

Alfa AF: 0.412 Hom.: 1194

Bravo AF: 0.484

Asia WGS AF: 0.425 AC: 1477 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	4.8
Dann	Benign	0.91

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: rs1683563; hg19: chr19-861593;