dbSNP rs9871864: SGO1-AS1:n.571-34386T>C (chr3-20311274-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000634618.1(SGO1-AS1):n.571-34386T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,052 control chromosomes in the GnomAD database, including 12,349 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 0.40 ( 12349 hom., cov: 33)

Consequence

SGO1-AS1
ENST00000634618.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.310

Publications

7 publications found

Variant links:

Genes affected

SGO1-AS1 (HGNC:41081): (SGO1 antisense RNA 1)

SGO1-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=-0.64).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 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
SGO1-AS1	ENST00000634618.1 link	n.571-34386T>C	intron_variant	Intron 4 of 16	5
SGO1-AS1	ENST00000736217.1 link	n.329-69901T>C	intron_variant	Intron 3 of 4
SGO1-AS1	ENST00000736218.1 link	n.275-69901T>C	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60199

AN:

151934

Hom.:

12342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.337

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.462

Gnomad OTH

AF:

0.381

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

GnomAD4 genome

AF:

0.396

AC:

60237

AN:

152052

Hom.:

12349

Cov.:

AF XY:

0.392

AC XY:

29121

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.337

AC:

13965

AN:

41474

American (AMR)

AF:

0.318

AC:

4857

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.429

AC:

1490

AN:

3470

East Asian (EAS)

AF:

0.269

AC:

1389

AN:

5166

South Asian (SAS)

AF:

0.304

AC:

1465

AN:

4826

European-Finnish (FIN)

AF:

0.416

AC:

4400

AN:

10570

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.462

AC:

31402

AN:

67964

Other (OTH)

AF:

0.378

AC:

796

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1865

3730

5596

7461

9326

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

582

1164

1746

2328

2910

<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:

0.445

Hom.:

17622

Bravo

AF:

0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

6.3

(source)

DANN

Benign

0.70

PhyloP100

0.31

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