dbSNP rs6000448: NCF4-AS1:n.381-6712C>T (chr22-36854729-G-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.381-6712C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,096 control chromosomes in the GnomAD database, including 3,605 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 ( 3605 hom., cov: 32)

Consequence

NCF4-AS1
ENST00000619915.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0730

Publications

1 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCF4-AS1	NR_147197.1 link	n.352-6712C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
NCF4-AS1	ENST00000619915.2 link	n.381-6712C>T	intron_variant	Intron 1 of 1	4
NCF4-AS1	ENST00000805861.1 link	n.355-6712C>T	intron_variant	Intron 1 of 2
NCF4-AS1	ENST00000805862.1 link	n.609+1583C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25863

AN:

151978

Hom.:

3594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.377

Gnomad AMI

AF:

0.124

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.0711

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0471

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.0836

Gnomad OTH

AF:

0.167

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

GnomAD4 genome

AF:

0.170

AC:

25909

AN:

152096

Hom.:

3605

Cov.:

AF XY:

0.167

AC XY:

12423

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.377

AC:

15624

AN:

41414

American (AMR)

AF:

0.138

AC:

2107

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

560

AN:

3468

East Asian (EAS)

AF:

0.0713

AC:

369

AN:

5176

South Asian (SAS)

AF:

0.113

AC:

547

AN:

4824

European-Finnish (FIN)

AF:

0.0471

AC:

500

AN:

10618

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0836

AC:

5687

AN:

67994

Other (OTH)

AF:

0.167

AC:

353

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

944

1889

2833

3778

4722

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.146

Hom.:

591

Bravo

AF:

0.184

Asia WGS

AF:

0.122

AC:

422

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.2

(source)

DANN

Benign

0.31

PhyloP100

-0.073

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