Genetic Variant NCF4-AS1:n.381-8625C>G (chr22-36856642-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000619915.2(NCF4-AS1):n.381-8625C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,208 control chromosomes in the GnomAD database, including 2,997 homozygotes. 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 0.15 ( 2997 hom., cov: 33)

Consequence

NCF4-AS1
ENST00000619915.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.199

Publications

6 publications found

Variant links:

Genes affected

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

NCF4-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1 link	n.352-8625C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NCF4-AS1	ENST00000619915.2 link	n.381-8625C>G	intron_variant	Intron 1 of 1	4
NCF4-AS1	ENST00000805861.1 link	n.355-8625C>G	intron_variant	Intron 1 of 2
NCF4-AS1	ENST00000805862.1 link	n.352-73C>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22357

AN:

152090

Hom.:

2984

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0874

Gnomad ASJ

AF:

0.0749

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.0783

Gnomad FIN

AF:

0.0207

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.0656

Gnomad OTH

AF:

0.130

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

GnomAD4 genome

AF:

0.147

AC:

22399

AN:

152208

Hom.:

2997

Cov.:

AF XY:

0.140

AC XY:

10454

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.356

AC:

14782

AN:

41498

American (AMR)

AF:

0.0872

AC:

1334

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0749

AC:

260

AN:

3472

East Asian (EAS)

AF:

0.100

AC:

518

AN:

5178

South Asian (SAS)

AF:

0.0784

AC:

378

AN:

4824

European-Finnish (FIN)

AF:

0.0207

AC:

220

AN:

10612

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0657

AC:

4465

AN:

68010

Other (OTH)

AF:

0.130

AC:

274

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

835

1669

2504

3338

4173

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.109

Hom.:

238

Bravo

AF:

0.160

Asia WGS

AF:

0.105

AC:

365

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.4

(source)

DANN

Benign

0.44

PhyloP100

-0.20

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over