rs9820712

Variant names:

• chr3-20665733-C-G
• rs9820712
• ENST00000634618.1:n.1378-33652C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634618.1(SGO1-AS1):​n.1378-33652C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,138 control chromosomes in the GnomAD database, including 16,284 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 0.46 (16284 hom., cov: 33)
• Consequence: SGO1-AS1 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.1378-33652C>G		intron_variant	Intron 10 of 16	5

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69302 AN: 152020 Hom.: 16259 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.456 AC: 69376 AN: 152138 Hom.: 16284 Cov.: 33 AF XY: 0.459 AC XY: 34123 AN XY: 74362

African (AFR) AF: 0.552 AC: 22907 AN: 41500

American (AMR) AF: 0.405 AC: 6195 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1288 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2134 AN: 5166

South Asian (SAS) AF: 0.434 AC: 2093 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5141 AN: 10578

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28280 AN: 67986

Other (OTH) AF: 0.428 AC: 904 AN: 2114

Alfa AF: 0.436 Hom.: 1847

Bravo AF: 0.453

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		0.045

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9820712; hg19: chr3-20707225;