ENST00000438382.2:n.368A>T

Variant names:

• chr7-75166663-T-A
• rs13447
• ENST00000438382.2:n.368A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000438382.2(NCF1C):​n.368A>T variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 4)
• Consequence: NCF1C ENST00000438382.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.24
• Publications: 7 publications found

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]

NCF1C (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438382.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF1C	NR_003187.3		n.322A>T		non_coding_transcript_exon	Exon 4 of 11

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCF1C	ENST00000438382.2	TSL:6	n.368A>T		non_coding_transcript_exon	Exon 4 of 11
	NCF1C	ENST00000740088.1		n.326A>T		non_coding_transcript_exon	Exon 4 of 11
	NCF1C	ENST00000740089.1		n.289A>T		non_coding_transcript_exon	Exon 4 of 10

Frequencies

GnomAD3 genomes Cov.: 4

GnomAD2 exomes AF: 0.00 AC: 0 AN: 222814 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 4

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		4.2

Splicing

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

Other links and lift over

dbSNP: rs13447; hg19: chr7-74582468;