rs886045650

Variant names:

• chr1-183555848-ACTCT-A
• rs886045650
• NM_000433.4:c.*266_*269delAGAG

Your query was ambiguous. Multiple possible variants found:

• chr1-183555848-ACTCT-A
• chr1-183555848-ACTCT-ACT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_000433.4(NCF2):​c.*266_*269delAGAG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000266 in 375,734 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: NCF2 NM_000433.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 0 publications found

Genes affected

NCF2 (HGNC:7661): (neutrophil cytosolic factor 2) This gene encodes neutrophil cytosolic factor 2, the 67-kilodalton cytosolic subunit of the multi-protein NADPH oxidase complex found in neutrophils. This oxidase produces a burst of superoxide which is delivered to the lumen of the neutrophil phagosome. Mutations in this gene, as well as in other NADPH oxidase subunits, can result in chronic granulomatous disease, a disease that causes recurrent infections by catalase-positive organisms. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2010]

SMG7 (HGNC:16792): (SMG7 nonsense mediated mRNA decay factor) This gene encodes a protein that is essential for nonsense-mediated mRNA decay (NMD); a process whereby transcripts with premature termination codons are targeted for rapid degradation by a mRNA decay complex. The mRNA decay complex consists, in part, of this protein along with proteins SMG5 and UPF1. The N-terminal domain of this protein is thought to mediate its association with SMG5 or UPF1 while the C-terminal domain interacts with the mRNA decay complex. This protein may therefore couple changes in UPF1 phosphorylation state to the degradation of NMD-candidate transcripts. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2011]

SMG7 Gene-Disease associations (from GenCC):

• autoimmune disease

  Inheritance: AD Classification: NO_KNOWN Submitted by: Illumina

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000433.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF2	NM_000433.4	MANE Select	c.*266_*269delAGAG		3_prime_UTR	Exon 15 of 15	NP_000424.2	P19878-1
	NCF2	NM_001127651.3		c.*266_*269delAGAG		3_prime_UTR	Exon 16 of 16	NP_001121123.1	P19878-1
	NCF2	NM_001410895.1		c.*266_*269delAGAG		3_prime_UTR	Exon 15 of 15	NP_001397824.1	A0A8V8TMB9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF2	ENST00000367535.8	TSL:1 MANE Select	c.*266_*269delAGAG		3_prime_UTR	Exon 15 of 15	ENSP00000356505.4	P19878-1
	NCF2	ENST00000367536.5	TSL:1	c.*266_*269delAGAG		3_prime_UTR	Exon 16 of 16	ENSP00000356506.1	P19878-1
	NCF2	ENST00000946295.1		c.*266_*269delAGAG		3_prime_UTR	Exon 16 of 16	ENSP00000616354.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000266 AC: 1 AN: 375734 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 198932

African (AFR) AF: 0.0000917 AC: 1 AN: 10906

American (AMR) AF: 0.00 AC: 0 AN: 16056

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11516

East Asian (EAS) AF: 0.00 AC: 0 AN: 24702

South Asian (SAS) AF: 0.00 AC: 0 AN: 43068

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22184

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1630

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 223958

Other (OTH) AF: 0.00 AC: 0 AN: 21714

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.017

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: rs886045650; hg19: chr1-183524983;