rs556679

chr6-31926578-C-T

Variant summary

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

The NM_001178063.3(C2):c.74-7032C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,766 control chromosomes in the GnomAD database, including 866 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 0.11 (866 hom., cov: 30)
• Consequence: C2 NM_001178063.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

Genes affected

C2 (HGNC:1248): (complement C2) Component C2 is a serum glycoprotein that functions as part of the classical pathway of the complement system. Activated C1 cleaves C2 into C2a and C2b. The serine proteinase C2a then combines with complement factor 4b to create the C3 or C5 convertase. Deficiency of C2 has been reported to associated with certain autoimmune diseases and SNPs in this gene have been associated with altered susceptibility to age-related macular degeneration. This gene localizes within the class III region of the MHC on the short arm of chromosome 6. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described in publications but their full-length sequence has not been determined.[provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2	NM_001178063.3	c.74-7032C>T		intron_variant
C2	NM_001282457.2	c.-63-7032C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2	ENST00000413154.5	c.-99-1076C>T		intron_variant		4
C2	ENST00000452202.5	c.74-7032C>T		intron_variant		4
C2	ENST00000452323.7	c.74-7032C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16167 AN: 151658 Hom.: 864 Cov.: 30

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0993

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.0272

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.107 AC: 16186 AN: 151766 Hom.: 866 Cov.: 30 AF XY: 0.105 AC XY: 7753 AN XY: 74164

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.0275

Gnomad4 SAS AF: 0.0748

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.115

Alfa AF: 0.104 Hom.: 102

Bravo AF: 0.108

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs556679; hg19: chr6-31894355;