NM_000631.5:c.-95C>T

Variant names:

• chr22-36861077-C-T
• rs148141762
• NM_000631.5:c.-95C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_000631.5(NCF4):​c.-95C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00242 in 1,499,536 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.013 (40 hom., cov: 32)
  • Exomes 𝑓: 0.0013 (39 hom.)
• Consequence: NCF4 NM_000631.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.69
• Publications: 0 publications found

Genes affected

NCF4 (HGNC:7662): (neutrophil cytosolic factor 4) The protein encoded by this gene is a cytosolic regulatory component of the superoxide-producing phagocyte NADPH-oxidase, a multicomponent enzyme system important for host defense. This protein is preferentially expressed in cells of myeloid lineage. It interacts primarily with neutrophil cytosolic factor 2 (NCF2/p67-phox) to form a complex with neutrophil cytosolic factor 1 (NCF1/p47-phox), which further interacts with the small G protein RAC1 and translocates to the membrane upon cell stimulation. This complex then activates flavocytochrome b, the membrane-integrated catalytic core of the enzyme system. The PX domain of this protein can bind phospholipid products of the PI(3) kinase, which suggests its role in PI(3) kinase-mediated signaling events. The phosphorylation of this protein was found to negatively regulate the enzyme activity. Alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

NCF4-AS1 (HGNC:40393): (NCF4 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 22-36861077-C-T is Benign according to our data. Variant chr22-36861077-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1318365.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0126 (1919/152226) while in subpopulation AFR AF = 0.0436 (1812/41528). AF 95% confidence interval is 0.042. There are 40 homozygotes in GnomAd4. There are 906 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 40 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4	NM_000631.5	c.-95C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10	ENST00000248899.11	NP_000622.2
NCF4	NM_000631.5	c.-95C>T		5_prime_UTR_variant	Exon 1 of 10	ENST00000248899.11	NP_000622.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCF4	ENST00000248899.11	c.-95C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 10	1	NM_000631.5	ENSP00000248899.6
NCF4	ENST00000248899.11	c.-95C>T		5_prime_UTR_variant	Exon 1 of 10	1	NM_000631.5	ENSP00000248899.6

Frequencies

GnomAD3 genomes AF: 0.0126 AC: 1920 AN: 152108 Hom.: 41 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00471

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: 0.000176

Gnomad OTH AF: 0.0110

GnomAD4 exome AF: 0.00127 AC: 1716 AN: 1347310 Hom.: 39 Cov.: 26 AF XY: 0.00111 AC XY: 743 AN XY: 667272

African (AFR) AF: 0.0436 AC: 1334 AN: 30586

American (AMR) AF: 0.00334 AC: 119 AN: 35632

Ashkenazi Jewish (ASJ) AF: 0.0000803 AC: 2 AN: 24900

East Asian (EAS) AF: 0.0000282 AC: 1 AN: 35486

South Asian (SAS) AF: 0.0000512 AC: 4 AN: 78120

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49180

Middle Eastern (MID) AF: 0.00104 AC: 5 AN: 4788

European-Non Finnish (NFE) AF: 0.0000872 AC: 90 AN: 1032396

Other (OTH) AF: 0.00286 AC: 161 AN: 56222

GnomAD4 genome AF: 0.0126 AC: 1919 AN: 152226 Hom.: 40 Cov.: 32 AF XY: 0.0122 AC XY: 906 AN XY: 74430

African (AFR) AF: 0.0436 AC: 1812 AN: 41528

American (AMR) AF: 0.00471 AC: 72 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5162

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000176 AC: 12 AN: 68008

Other (OTH) AF: 0.0109 AC: 23 AN: 2112

Alfa AF: 0.0112 Hom.: 5

Bravo AF: 0.0146

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 20, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
DANN	Benign	0.66
PhyloP100		-2.7
PromoterAI		-0.10	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs148141762; hg19: chr22-37257119;