rs497239

Positions:

• chr6-31940984-T-C

Variant summary

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

The NM_000063.6(C2):​c.1219+1664T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,174 control chromosomes in the GnomAD database, including 1,220 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 0.12 (1220 hom., cov: 32)
• Consequence: C2 NM_000063.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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]

C2-AS1 (HGNC:49464): (C2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2	NM_000063.6	c.1219+1664T>C		intron_variant		ENST00000299367.10
C2-AS1	NR_104191.1	n.540+201A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2	ENST00000299367.10	c.1219+1664T>C		intron_variant		1	NM_000063.6	P1
C2-AS1	ENST00000630806.1	n.540+201A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17801 AN: 152056 Hom.: 1222 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.117 AC: 17822 AN: 152174 Hom.: 1220 Cov.: 32 AF XY: 0.115 AC XY: 8555 AN XY: 74412

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0574

Gnomad4 EAS AF: 0.0593

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0574

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0873 Hom.: 833

Bravo AF: 0.124

Asia WGS AF: 0.155 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.52

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: rs497239; hg19: chr6-31908761;