dbSNP rs10483474: ENSG00000283098:n.323-57769G>A (chr14-36596980-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 ENST00000634305.1(ENSG00000283098):n.323-57769G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 151,966 control chromosomes in the GnomAD database, including 760 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 0.058 ( 760 hom., cov: 32)

Consequence

ENSG00000283098
ENST00000634305.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.445

Publications

0 publications found

Variant links:

Genes affected

ENSG00000283098 (HGNC:):

ENSG00000283098 links:

NKX2-1-AS1 (HGNC:40585): (NKX2-1 antisense RNA 1)

NKX2-1-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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000283098	ENST00000634305.1 link	n.323-57769G>A	intron_variant	Intron 3 of 3	5
NKX2-1-AS1	ENST00000716761.1 link	n.270+36367G>A	intron_variant	Intron 2 of 2
NKX2-1-AS1	ENST00000716763.1 link	n.771+24735G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0583

AC:

8846

AN:

151848

Hom.:

757

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0237

Gnomad ASJ

AF:

0.0600

Gnomad EAS

AF:

0.00232

Gnomad SAS

AF:

0.0227

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00277

Gnomad OTH

AF:

0.0417

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

GnomAD4 genome

AF:

0.0583

AC:

8864

AN:

151966

Hom.:

760

Cov.:

AF XY:

0.0567

AC XY:

4212

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.191

AC:

7897

AN:

41408

American (AMR)

AF:

0.0236

AC:

360

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0600

AC:

208

AN:

3464

East Asian (EAS)

AF:

0.00232

AC:

AN:

5168

South Asian (SAS)

AF:

0.0221

AC:

106

AN:

4798

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10590

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00277

AC:

188

AN:

67954

Other (OTH)

AF:

0.0417

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

376

752

1128

1504

1880

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0411

Hom.:

Bravo

AF:

0.0663

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.4

(source)

DANN

Benign

0.75

PhyloP100

0.45

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