chr5-40965216-C-T

Position:

• chr5-40965216-C-T

Variant summary

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

The NM_000587.4(C7):​c.1882+343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,110 control chromosomes in the GnomAD database, including 3,722 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 0.20 (3722 hom., cov: 32)
• Consequence: C7 NM_000587.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

C7 (HGNC:1346): (complement C7) This gene encodes a serum glycoprotein that forms a membrane attack complex together with complement components C5b, C6, C8, and C9 as part of the terminal complement pathway of the innate immune system. The protein encoded by this gene contains a cholesterol-dependent cytolysin/membrane attack complex/perforin-like (CDC/MACPF) domain and belongs to a large family of structurally related molecules that form pores involved in host immunity and bacterial pathogenesis. This protein initiates membrane attack complex formation by binding the C5b-C6 subcomplex and inserts into the phospholipid bilayer, serving as a membrane anchor. Mutations in this gene are associated with a rare disorder called C7 deficiency. [provided by RefSeq, Nov 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C7	NM_000587.4	c.1882+343C>T		intron_variant		ENST00000313164.10	NP_000578.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C7	ENST00000313164.10	c.1882+343C>T		intron_variant		1	NM_000587.4	ENSP00000322061	P1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29895 AN: 151994 Hom.: 3722 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.197 AC: 29904 AN: 152110 Hom.: 3722 Cov.: 32 AF XY: 0.202 AC XY: 15044 AN XY: 74346

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.200

Alfa AF: 0.246 Hom.: 2477

Bravo AF: 0.181

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.18

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: rs3805221; hg19: chr5-40965318;