dbSNP rs752590: PAX8-AS1:n.99-788A>G (chr2-113215368-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 ENST00000456685.5(PAX8-AS1):n.99-788A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,986 control chromosomes in the GnomAD database, including 5,933 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 0.26 ( 5933 hom., cov: 32)

Consequence

PAX8-AS1
ENST00000456685.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.966

Publications

26 publications found

Variant links:

Genes affected

PAX8-AS1 (HGNC:49271): (PAX8 antisense RNA 1)

PAX8-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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 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
PAX8-AS1	ENST00000456685.5 link	n.99-788A>G	intron_variant	Intron 1 of 5	1
PAX8-AS1	ENST00000662215.1 link	n.199+3749A>G	intron_variant	Intron 1 of 3
PAX8-AS1	ENST00000777999.1 link	n.141+3749A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40029

AN:

151868

Hom.:

5915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.411

Gnomad AMI

AF:

0.335

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.213

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

GnomAD4 genome

AF:

0.264

AC:

40092

AN:

151986

Hom.:

5933

Cov.:

AF XY:

0.262

AC XY:

19462

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.411

AC:

16994

AN:

41394

American (AMR)

AF:

0.187

AC:

2866

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

573

AN:

3470

East Asian (EAS)

AF:

0.159

AC:

824

AN:

5176

South Asian (SAS)

AF:

0.144

AC:

695

AN:

4822

European-Finnish (FIN)

AF:

0.275

AC:

2903

AN:

10568

Middle Eastern (MID)

AF:

0.137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.212

AC:

14441

AN:

67960

Other (OTH)

AF:

0.214

AC:

451

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1453

2905

4358

5810

7263

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.221

Hom.:

4289

Bravo

AF:

0.263

Asia WGS

AF:

0.202

AC:

702

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.2

(source)

DANN

Benign

0.60

PhyloP100

-0.97

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