rs9871864

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.571-34386T>C		intron_variant	Intron 4 of 16	5

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

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.378

Alfa AF: 0.444 Hom.: 12002

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
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9871864; hg19: chr3-20352766;