NM_000587.4:c.138+573G>A

Variant names:

• chr5-40931712-G-A
• rs10512750
• NM_000587.4:c.138+573G>A

Variant summary

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

The NM_000587.4(C7):​c.138+573G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,198 control chromosomes in the GnomAD database, including 2,687 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 0.18 (2687 hom., cov: 33)
• Consequence: C7 NM_000587.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 3 publications found

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]

C7 Gene-Disease associations (from GenCC):

• complement component 7 deficiency

  Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics, Illumina, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C7	NM_000587.4	c.138+573G>A		intron_variant	Intron 3 of 17	ENST00000313164.10	NP_000578.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C7	ENST00000313164.10	c.138+573G>A		intron_variant	Intron 3 of 17	1	NM_000587.4	ENSP00000322061.9

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27409 AN: 152080 Hom.: 2681 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.180 AC: 27436 AN: 152198 Hom.: 2687 Cov.: 33 AF XY: 0.183 AC XY: 13597 AN XY: 74422

African (AFR) AF: 0.108 AC: 4501 AN: 41542

American (AMR) AF: 0.222 AC: 3400 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1634 AN: 5176

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4826

European-Finnish (FIN) AF: 0.188 AC: 1989 AN: 10594

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13552 AN: 67990

Other (OTH) AF: 0.173 AC: 366 AN: 2114

Alfa AF: 0.193 Hom.: 795

Bravo AF: 0.180

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.59
PhyloP100		-0.38
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: rs10512750; hg19: chr5-40931814;