rs9871864

Positions:

• chr3-20311274-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.571-34386T>C		intron_variant, non_coding_transcript_variant		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;