Genetic Variant SGO1-AS1:n.1727+10357G>C (chr3-20858640-G-C) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000634618.1(SGO1-AS1):n.1727+10357G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,162 control chromosomes in the GnomAD database, including 1,578 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 ( 1578 hom., cov: 33)

Consequence

SGO1-AS1
ENST00000634618.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.376

Publications

3 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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.1727+10357G>C	intron_variant	Intron 14 of 16	5
SGO1-AS1	ENST00000634837.1 link	n.118-11649G>C	intron_variant	Intron 1 of 7	5
SGO1-AS1	ENST00000837212.1 link	n.91-11649G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16532

AN:

152044

Hom.:

1573

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.0787

Gnomad EAS

AF:

0.396

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.0806

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0610

Gnomad OTH

AF:

0.114

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

GnomAD4 genome

AF:

0.109

AC:

16560

AN:

152162

Hom.:

1578

Cov.:

AF XY:

0.115

AC XY:

8531

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.106

AC:

4419

AN:

41520

American (AMR)

AF:

0.254

AC:

3875

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0787

AC:

273

AN:

3470

East Asian (EAS)

AF:

0.396

AC:

2042

AN:

5162

South Asian (SAS)

AF:

0.133

AC:

642

AN:

4818

European-Finnish (FIN)

AF:

0.0806

AC:

854

AN:

10600

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0610

AC:

4149

AN:

67998

Other (OTH)

AF:

0.114

AC:

241

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

685

1370

2055

2740

3425

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0282

Hom.:

Bravo

AF:

0.128

Asia WGS

AF:

0.255

AC:

884

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.38

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