19-6685806-G-C

Variant names:

• chr19-6685806-G-C
• rs344548
• NM_000064.4:c.3810+318C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000064.4(C3):​c.3810+318C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,024 control chromosomes in the GnomAD database, including 48,796 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 0.80 (48796 hom., cov: 30)
• Consequence: C3 NM_000064.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 13 publications found

Genes affected

C3 (HGNC:1318): (complement C3) Complement component C3 plays a central role in the activation of complement system. Its activation is required for both classical and alternative complement activation pathways. The encoded preproprotein is proteolytically processed to generate alpha and beta subunits that form the mature protein, which is then further processed to generate numerous peptide products. The C3a peptide, also known as the C3a anaphylatoxin, modulates inflammation and possesses antimicrobial activity. Mutations in this gene are associated with atypical hemolytic uremic syndrome and age-related macular degeneration in human patients. [provided by RefSeq, Nov 2015]

C3 Gene-Disease associations (from GenCC):

• atypical hemolytic-uremic syndrome with C3 anomaly

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• complement component 3 deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Laboratory for Molecular Medicine
• C3 glomerulonephritis

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen

ENSG00000297005 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000064.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3	NM_000064.4	MANE Select	c.3810+318C>G		intron	N/A	NP_000055.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C3	ENST00000245907.11	TSL:1 MANE Select	c.3810+318C>G		intron	N/A	ENSP00000245907.4
	C3	ENST00000695654.1		c.2835+318C>G		intron	N/A	ENSP00000512085.1
	C3	ENST00000695653.1		c.1719+318C>G		intron	N/A	ENSP00000512084.1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121167 AN: 151906 Hom.: 48778 Cov.: 30

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.797 AC: 121230 AN: 152024 Hom.: 48796 Cov.: 30 AF XY: 0.800 AC XY: 59428 AN XY: 74318

African (AFR) AF: 0.679 AC: 28127 AN: 41430

American (AMR) AF: 0.867 AC: 13241 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2983 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4737 AN: 5150

South Asian (SAS) AF: 0.829 AC: 3984 AN: 4808

European-Finnish (FIN) AF: 0.869 AC: 9203 AN: 10590

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56336 AN: 67986

Other (OTH) AF: 0.815 AC: 1718 AN: 2108

Alfa AF: 0.802 Hom.: 5754

Bravo AF: 0.795

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		0.028
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs344548; hg19: chr19-6685817;