Genetic Variant SATB1-AS1:n.205-20042C>T (chr3-18725912-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000425799.7(SATB1-AS1):n.205-20042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,060 control chromosomes in the GnomAD database, including 1,089 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 0.11 ( 1089 hom., cov: 32)

Consequence

SATB1-AS1
ENST00000425799.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.19

Publications

36 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 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	ENST00000425799.7 link	n.205-20042C>T	intron_variant	Intron 3 of 8	5
SATB1-AS1	ENST00000595388.5 link	n.365-20042C>T	intron_variant	Intron 3 of 4	5
SATB1-AS1	ENST00000626982.2 link	n.196-20042C>T	intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17321

AN:

151942

Hom.:

1089

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0590

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.0978

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.108

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

GnomAD4 genome

AF:

0.114

AC:

17326

AN:

152060

Hom.:

1089

Cov.:

AF XY:

0.112

AC XY:

8318

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.0589

AC:

2445

AN:

41476

American (AMR)

AF:

0.110

AC:

1673

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

500

AN:

3472

East Asian (EAS)

AF:

0.137

AC:

710

AN:

5166

South Asian (SAS)

AF:

0.0979

AC:

471

AN:

4810

European-Finnish (FIN)

AF:

0.111

AC:

1174

AN:

10586

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.146

AC:

9947

AN:

67966

Other (OTH)

AF:

0.108

AC:

227

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

768

1535

2303

3070

3838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.129

Hom.:

2747

Bravo

AF:

0.110

Asia WGS

AF:

0.106

AC:

370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

2.2

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