7-75166663-T-C

Position:

• chr7-75166663-T-C

Variant summary

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

The NR_003187.3(NCF1C):​n.322A>G variant causes a non coding transcript exon change. 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 0.00014 (0 hom., cov: 4)
  • Exomes 𝑓: 0.0024 (49 hom.)
  • Failed GnomAD Quality Control
• Consequence: NCF1C NR_003187.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.24

Genes affected

NCF1C (HGNC:32523): (neutrophil cytosolic factor 1C (pseudogene)) The neutrophil cytosolic factor 1 (NCF1) gene encodes the 47 kDa cytosolic subunit of neutrophil NADPH oxidase, which produces superoxide anion. The NCF1 gene is located in close proximity to two highly similar, multi-exon pseudogenes at chromosome 7q11.23, corresponding to this gene record and GeneID:654816. The two pseudogenes contain a dinucleotide deletion (delta-GT) in exon 2 that results in a frameshift and truncation of the open reading frame, and neither pseudogene is likely to express a protein. Recombination events between the pseudogenes and the functional NCF1 gene can inactivate the NCF1 gene and result in chronic granulomatous disease. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NCF1C	NR_003187.3	n.322A>G		non_coding_transcript_exon_variant	4/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NCF1C	ENST00000438382.2	n.368A>G		non_coding_transcript_exon_variant	4/11

Frequencies

GnomAD3 genomes AF: 0.00 AC: 6 AN: 42350 Hom.: 0 Cov.: 4 FAILED QC

Gnomad AFR AF: 0.000116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000316

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: 0.000183

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0193 AC: 4297 AN: 222814 Hom.: 630 AF XY: 0.0171 AC XY: 2076 AN XY: 121518

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.0139

Gnomad ASJ exome AF: 0.0148

Gnomad EAS exome AF: 0.0138

Gnomad SAS exome AF: 0.00806

Gnomad FIN exome AF: 0.0116

Gnomad NFE exome AF: 0.0122

Gnomad OTH exome AF: 0.0211

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00235 AC: 2958 AN: 1257140 Hom.: 49 Cov.: 31 AF XY: 0.00251 AC XY: 1567 AN XY: 624628

Gnomad4 AFR exome AF: 0.00356

Gnomad4 AMR exome AF: 0.00382

Gnomad4 ASJ exome AF: 0.00514

Gnomad4 EAS exome AF: 0.00176

Gnomad4 SAS exome AF: 0.00607

Gnomad4 FIN exome AF: 0.00207

Gnomad4 NFE exome AF: 0.00190

Gnomad4 OTH exome AF: 0.00289

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000141 AC: 6 AN: 42422 Hom.: 0 Cov.: 4 AF XY: 0.000150 AC XY: 3 AN XY: 20040

Gnomad4 AFR AF: 0.000116

Gnomad4 AMR AF: 0.000315

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000183

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0199 Hom.: 45

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
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: rs13447; hg19: chr7-74582468;