Genetic Variant SATB1-AS1:n.609+13030G>T (chr3-18540356-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000456253.6(SATB1-AS1):n.609+13030G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,044 control chromosomes in the GnomAD database, including 5,642 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 0.23 ( 5642 hom., cov: 32)

Consequence

SATB1-AS1
ENST00000456253.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.315

Publications

5 publications found

Variant links:

COSMIC-nc: COSV69863005

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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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	ENST00000456253.6 link	n.609+13030G>T	intron_variant	Intron 5 of 6	5
SATB1-AS1	ENST00000595250.5 link	n.461+13030G>T	intron_variant	Intron 4 of 4	5
SATB1-AS1	ENST00000595388.5 link	n.364+13030G>T	intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35422

AN:

151926

Hom.:

5618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.205

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

GnomAD4 genome

AF:

0.233

AC:

35493

AN:

152044

Hom.:

5642

Cov.:

AF XY:

0.238

AC XY:

17694

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.413

AC:

17114

AN:

41452

American (AMR)

AF:

0.326

AC:

4987

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

563

AN:

3470

East Asian (EAS)

AF:

0.354

AC:

1828

AN:

5160

South Asian (SAS)

AF:

0.232

AC:

1119

AN:

4816

European-Finnish (FIN)

AF:

0.183

AC:

1932

AN:

10584

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7358

AN:

67972

Other (OTH)

AF:

0.209

AC:

442

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1214

2428

3642

4856

6070

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.145

Hom.:

3991

Bravo

AF:

0.252

Asia WGS

AF:

0.307

AC:

1063

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.5

(source)

DANN

Benign

0.58

PhyloP100

0.32

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