dbSNP rs11128951: SGO1-AS1:n.571-11606A>G (chr3-20334054-A-G) – 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.571-11606A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,920 control chromosomes in the GnomAD database, including 3,000 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 0.19 ( 3000 hom., cov: 32)

Consequence

SGO1-AS1
ENST00000634618.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.288

Publications

8 publications found

Variant links:

Genes affected

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

SGO1-AS1 links:

ENSG00000296099 (HGNC:):

ENSG00000296099 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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) 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
SGO1-AS1	ENST00000634618.1 link	n.571-11606A>G	intron_variant	Intron 4 of 16	5
SGO1-AS1	ENST00000736217.1 link	n.329-47121A>G	intron_variant	Intron 3 of 4
SGO1-AS1	ENST00000736218.1 link	n.275-47121A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29403

AN:

151804

Hom.:

2992

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.198

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.199

Gnomad OTH

AF:

0.200

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

GnomAD4 genome

AF:

0.194

AC:

29423

AN:

151920

Hom.:

3000

Cov.:

AF XY:

0.196

AC XY:

14557

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.148

AC:

6130

AN:

41404

American (AMR)

AF:

0.237

AC:

3618

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

500

AN:

3466

East Asian (EAS)

AF:

0.347

AC:

1794

AN:

5164

South Asian (SAS)

AF:

0.239

AC:

1149

AN:

4810

European-Finnish (FIN)

AF:

0.198

AC:

2091

AN:

10570

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.199

AC:

13494

AN:

67928

Other (OTH)

AF:

0.204

AC:

431

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1207

2414

3620

4827

6034

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.190

Hom.:

2342

Bravo

AF:

0.195

Asia WGS

AF:

0.275

AC:

950

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

0.29

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