dbSNP rs5995355: NCF4-AS1:n.381-7402T>C (chr22-36855419-A-G) – 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.381-7402T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,252 control chromosomes in the GnomAD database, including 3,675 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 0.16 ( 3675 hom., cov: 33)

Consequence

NCF4-AS1
ENST00000619915.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0100

Publications

9 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1 link	n.352-7402T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NCF4-AS1	ENST00000619915.2 link	n.381-7402T>C	intron_variant	Intron 1 of 1	4
NCF4-AS1	ENST00000805861.1 link	n.355-7402T>C	intron_variant	Intron 1 of 2
NCF4-AS1	ENST00000805862.1 link	n.609+893T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24836

AN:

152134

Hom.:

3665

Cov.:

show subpopulations

Gnomad AFR

AF:

0.391

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.0723

Gnomad SAS

AF:

0.0860

Gnomad FIN

AF:

0.0361

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0670

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.163

AC:

24874

AN:

152252

Hom.:

3675

Cov.:

AF XY:

0.160

AC XY:

11901

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.391

AC:

16215

AN:

41490

American (AMR)

AF:

0.132

AC:

2016

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

432

AN:

3472

East Asian (EAS)

AF:

0.0720

AC:

374

AN:

5192

South Asian (SAS)

AF:

0.0853

AC:

412

AN:

4832

European-Finnish (FIN)

AF:

0.0361

AC:

383

AN:

10624

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0670

AC:

4559

AN:

68018

Other (OTH)

AF:

0.157

AC:

331

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

916

1831

2747

3662

4578

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.0864

Hom.:

390

Bravo

AF:

0.179

Asia WGS

AF:

0.111

AC:

383

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.3

(source)

DANN

Benign

0.35

PhyloP100

0.010

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