Genetic Variant SATB1-AS1:n.365-80588G>A (chr3-18665366-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 ENST00000595388.5(SATB1-AS1):n.365-80588G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,956 control chromosomes in the GnomAD database, including 5,408 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 0.25 ( 5408 hom., cov: 32)

Consequence

SATB1-AS1
ENST00000595388.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.498

Publications

33 publications found

Variant links:

Genes affected

SATB1-AS1 (HGNC:50687): (SATB1 antisense RNA 1)

SATB1-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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 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
SATB1-AS1	ENST00000595388.5 link	n.365-80588G>A	intron_variant	Intron 3 of 4	5
SATB1-AS1	ENST00000626982.2 link	n.196-80588G>A	intron_variant	Intron 2 of 4	5
SATB1-AS1	ENST00000627192.2 link	n.365-80588G>A	intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37549

AN:

151836

Hom.:

5407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.414

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.0253

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.282

Gnomad MID

AF:

0.349

Gnomad NFE

AF:

0.338

Gnomad OTH

AF:

0.257

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

GnomAD4 genome

AF:

0.247

AC:

37560

AN:

151956

Hom.:

5408

Cov.:

AF XY:

0.243

AC XY:

18053

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.121

AC:

5000

AN:

41460

American (AMR)

AF:

0.219

AC:

3350

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.293

AC:

1015

AN:

3468

East Asian (EAS)

AF:

0.0256

AC:

132

AN:

5162

South Asian (SAS)

AF:

0.235

AC:

1130

AN:

4812

European-Finnish (FIN)

AF:

0.282

AC:

2967

AN:

10534

Middle Eastern (MID)

AF:

0.345

AC:

100

AN:

290

European-Non Finnish (NFE)

AF:

0.338

AC:

22953

AN:

67940

Other (OTH)

AF:

0.254

AC:

535

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1400

2800

4199

5599

6999

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.299

Hom.:

25593

Bravo

AF:

0.237

Asia WGS

AF:

0.109

AC:

380

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.2

(source)

DANN

Benign

0.84

PhyloP100

-0.50

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