dbSNP rs1983667: ENSG00000283098:n.323-25766A>T (chr14-36628983-A-T) – 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.323-25766A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,084 control chromosomes in the GnomAD database, including 1,099 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 0.087 ( 1099 hom., cov: 32)

Consequence

ENSG00000283098
ENST00000634305.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.187

Publications

2 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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.323-25766A>T	intron_variant	Intron 3 of 3	5
NKX2-1-AS1	ENST00000716761.1 link	n.271-25766A>T	intron_variant	Intron 2 of 2
NKX2-1-AS1	ENST00000716763.1 link	n.772-25766A>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0870

AC:

13226

AN:

151968

Hom.:

1096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.227

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.0435

Gnomad ASJ

AF:

0.0297

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0218

Gnomad FIN

AF:

0.0345

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0357

Gnomad OTH

AF:

0.0718

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

GnomAD4 genome

AF:

0.0871

AC:

13241

AN:

152084

Hom.:

1099

Cov.:

AF XY:

0.0846

AC XY:

6294

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.227

AC:

9394

AN:

41414

American (AMR)

AF:

0.0434

AC:

663

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0297

AC:

103

AN:

3466

East Asian (EAS)

AF:

0.000580

AC:

AN:

5174

South Asian (SAS)

AF:

0.0212

AC:

102

AN:

4814

European-Finnish (FIN)

AF:

0.0345

AC:

366

AN:

10618

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0357

AC:

2427

AN:

68002

Other (OTH)

AF:

0.0710

AC:

150

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

560

1120

1679

2239

2799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.0611

Hom.:

Bravo

AF:

0.0949

Asia WGS

AF:

0.0200

AC:

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

1.5

(source)

DANN

Benign

0.36

PhyloP100

0.19

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