3-20311274-T-C

Variant names:

• chr3-20311274-T-C
• rs9871864
• ENST00000634618.1:n.571-34386T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 7 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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634618.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGO1-AS1	ENST00000634618.1	TSL:5	n.571-34386T>C		intron	N/A
	SGO1-AS1	ENST00000736217.1		n.329-69901T>C		intron	N/A
	SGO1-AS1	ENST00000736218.1		n.275-69901T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60199 AN: 151934 Hom.: 12342 Cov.: 33

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.: 33 AF XY: 0.392 AC XY: 29121 AN XY: 74304

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

Alfa AF: 0.445 Hom.: 17622

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.3
DANN	Benign	0.70
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9871864; hg19: chr3-20352766;