rs1625859

Variant names:

• chr7-73225405-A-G
• rs1625859
• ENST00000423083.1:n.158+1449A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000423083.1(NCF1B):​n.158+1449A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00015 (0 hom., cov: 14)
• Consequence: NCF1B ENST00000423083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 publications found

Genes affected

NCF1B (HGNC:):

NCF1B (HGNC:32522): (neutrophil cytosolic factor 1B (pseudogene)) Predicted to enable superoxide-generating NADPH oxidase activator activity. Predicted to be involved in respiratory burst and superoxide anion generation. Predicted to be part of NADPH oxidase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423083.1. 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
	NCF1B	NR_003186.1		n.158+1449A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF1B	ENST00000423083.1	TSL:2	n.158+1449A>G		intron	N/A
	NCF1B	ENST00000432102.5	TSL:2	n.174-306A>G		intron	N/A
	NCF1B	ENST00000435988.2	TSL:6	n.152-306A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000147 AC: 16 AN: 109006 Hom.: 0 Cov.: 14

Gnomad AFR AF: 0.000334

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000258

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000219

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000104

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000147 AC: 16 AN: 109076 Hom.: 0 Cov.: 14 AF XY: 0.000134 AC XY: 7 AN XY: 52086

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000332 AC: 6 AN: 18066

American (AMR) AF: 0.000257 AC: 3 AN: 11668

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3008

East Asian (EAS) AF: 0.000219 AC: 1 AN: 4562

South Asian (SAS) AF: 0.00 AC: 0 AN: 3434

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8130

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 244

European-Non Finnish (NFE) AF: 0.000104 AC: 6 AN: 57674

Other (OTH) AF: 0.00 AC: 0 AN: 1456

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000000000000555111), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0121 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	2.8
DANN	Benign	0.79
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1625859;

hg19: chr7-72639440;