6-31915902-C-T

Position:

• chr6-31915902-C-T

Variant summary

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

The ENST00000695637.1(C2):​c.-359-12053C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,254 control chromosomes in the GnomAD database, including 1,313 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 (1313 hom., cov: 32)
• Consequence: C2 ENST00000695637.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2	NM_001178063.3	c.73+14763C>T		intron_variant			NP_001171534.1
C2	NM_001282457.2	c.-63-17708C>T		intron_variant			NP_001269386.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2	ENST00000452202.5	c.73+14763C>T		intron_variant		4		ENSP00000406121
C2	ENST00000452323.7	c.73+14763C>T		intron_variant		2		ENSP00000392322
C2	ENST00000469372.5	c.-63-17708C>T		intron_variant		2		ENSP00000418923

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18158 AN: 152136 Hom.: 1313 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0921

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.119 AC: 18179 AN: 152254 Hom.: 1313 Cov.: 32 AF XY: 0.119 AC XY: 8841 AN XY: 74448

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.0954

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.0921

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0980 Hom.: 1103

Bravo AF: 0.123

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9267673; hg19: chr6-31883679;