5-39368074-A-G

Variant names:

• chr5-39368074-A-G
• rs700237
• ENST00000509186.6:c.5+3169T>C

Variant summary

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

The ENST00000509186.6(C9):​c.5+3169T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,444 control chromosomes in the GnomAD database, including 10,408 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 0.36 (10408 hom., cov: 31)
• Consequence: C9 ENST00000509186.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574
• Publications: 12 publications found

Genes affected

C9 (HGNC:1358): (complement C9) This gene encodes the final component of the complement system. It participates in the formation of the Membrane Attack Complex (MAC). The MAC assembles on bacterial membranes to form a pore, permitting disruption of bacterial membrane organization. Mutations in this gene cause component C9 deficiency. [provided by RefSeq, Feb 2009]

C9 Gene-Disease associations (from GenCC):

• complement component 9 deficiency

  Inheritance: Unknown, AR Classification: STRONG, MODERATE Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Ambry Genetics

ENSG00000289699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509186.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C9	ENST00000509186.6	TSL:3	c.5+3169T>C		intron	N/A	ENSP00000512235.1
	ENSG00000289699	ENST00000696106.1		n.119+20725T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54494 AN: 151350 Hom.: 10416 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.0710

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.360 AC: 54488 AN: 151444 Hom.: 10408 Cov.: 31 AF XY: 0.360 AC XY: 26595 AN XY: 73964

African (AFR) AF: 0.255 AC: 10550 AN: 41342

American (AMR) AF: 0.402 AC: 6122 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1627 AN: 3464

East Asian (EAS) AF: 0.0711 AC: 368 AN: 5174

South Asian (SAS) AF: 0.361 AC: 1731 AN: 4798

European-Finnish (FIN) AF: 0.377 AC: 3888 AN: 10306

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28792 AN: 67856

Other (OTH) AF: 0.420 AC: 876 AN: 2088

Alfa AF: 0.381 Hom.: 1792

Bravo AF: 0.356

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs700237; hg19: chr5-39368176;