dbSNP rs9680849: NCF4-AS1:n.381-6398A>T (chr22-36854415-T-A) – 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.381-6398A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,894 control chromosomes in the GnomAD database, including 3,491 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 0.17 ( 3491 hom., cov: 32)

Consequence

NCF4-AS1
ENST00000619915.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.210

Publications

2 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1 link	n.352-6398A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NCF4-AS1	ENST00000619915.2 link	n.381-6398A>T	intron_variant	Intron 1 of 1	4
NCF4-AS1	ENST00000805861.1 link	n.355-6398A>T	intron_variant	Intron 1 of 2
NCF4-AS1	ENST00000805862.1 link	n.609+1897A>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25544

AN:

151778

Hom.:

3480

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.0709

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0465

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.0832

Gnomad OTH

AF:

0.166

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

GnomAD4 genome

AF:

0.168

AC:

25589

AN:

151894

Hom.:

3491

Cov.:

AF XY:

0.166

AC XY:

12292

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.372

AC:

15361

AN:

41252

American (AMR)

AF:

0.137

AC:

2098

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.160

AC:

556

AN:

3466

East Asian (EAS)

AF:

0.0710

AC:

368

AN:

5182

South Asian (SAS)

AF:

0.113

AC:

544

AN:

4818

European-Finnish (FIN)

AF:

0.0465

AC:

492

AN:

10584

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0832

AC:

5658

AN:

67996

Other (OTH)

AF:

0.167

AC:

351

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

886

1773

2659

3546

4432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.135

Hom.:

278

Bravo

AF:

0.183

Asia WGS

AF:

0.121

AC:

420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.2

(source)

DANN

Benign

0.84

PhyloP100

-0.21

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