chr1-183556317-T-A

Variant names:

• chr1-183556317-T-A
• rs699244
• NM_000433.4:c.1469-87A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_000433.4(NCF2):​c.1469-87A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,218,508 control chromosomes in the GnomAD database, including 33 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 0.0094 (18 hom., cov: 31)
  • Exomes 𝑓: 0.00096 (15 hom.)
• Consequence: NCF2 NM_000433.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00943 (1436/152228) while in subpopulation AFR AF = 0.0329 (1365/41524). AF 95% confidence interval is 0.0314. There are 18 homozygotes in GnomAd4. There are 669 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF2	NM_000433.4	c.1469-87A>T		intron_variant	Intron 14 of 14	ENST00000367535.8	NP_000424.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCF2	ENST00000367535.8	c.1469-87A>T		intron_variant	Intron 14 of 14	1	NM_000433.4	ENSP00000356505.4

Frequencies

GnomAD3 genomes AF: 0.00941 AC: 1431 AN: 152110 Hom.: 18 Cov.: 31

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00334

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00813

GnomAD4 exome AF: 0.000960 AC: 1024 AN: 1066280 Hom.: 15 AF XY: 0.000783 AC XY: 428 AN XY: 546720

Gnomad4 AFR exome AF: 0.0315 AC: 812 AN: 25792

Gnomad4 AMR exome AF: 0.00168 AC: 71 AN: 42162

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 23482

Gnomad4 EAS exome AF: 0.0000266 AC: 1 AN: 37656

Gnomad4 SAS exome AF: 0.0000260 AC: 2 AN: 77020

Gnomad4 FIN exome AF: 0.0000195 AC: 1 AN: 51176

Gnomad4 NFE exome AF: 0.0000278 AC: 21 AN: 756672

Gnomad4 Remaining exome AF: 0.00235 AC: 111 AN: 47286

GnomAD4 genome AF: 0.00943 AC: 1436 AN: 152228 Hom.: 18 Cov.: 31 AF XY: 0.00899 AC XY: 669 AN XY: 74430

Gnomad4 AFR AF: 0.0329 AC: 0.0328726 AN: 0.0328726

Gnomad4 AMR AF: 0.00333 AC: 0.00333333 AN: 0.00333333

Gnomad4 ASJ AF: 0.00 AC: 0 AN: 0

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00 AC: 0 AN: 0

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.0000441 AC: 0.0000441086 AN: 0.0000441086

Gnomad4 OTH AF: 0.00804 AC: 0.00804163 AN: 0.00804163

Alfa AF: 0.00 Hom.: 4649

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.88
DANN	Benign	0.19
Mutation Taster		=100/0	polymorphism

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: rs699244; hg19: chr1-183525452;