rs1625859

Positions:

• chr7-73225405-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_003186.1(NCF1B):​n.158+1449A>G variant causes a intron, non coding transcript 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 NR_003186.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

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

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCF1B	NR_003186.1	n.158+1449A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCF1B	ENST00000423083.1	n.158+1449A>G		intron_variant, non_coding_transcript_variant		2
NCF1B	ENST00000435988.1	n.154-306A>G		intron_variant, non_coding_transcript_variant
NCF1B	ENST00000432102.5	n.174-306A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.000332

Gnomad4 AMR AF: 0.000257

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000219

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000104

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0121 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1625859; hg19: chr7-72639440;