rs11128951

Variant names:

• chr3-20334054-A-G
• rs11128951
• ENST00000634618.1:n.571-11606A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-20334054-A-G
• chr3-20334054-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

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=-0.75).
• 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	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.571-11606A>G		intron_variant	Intron 4 of 16	5

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29403 AN: 151804 Hom.: 2992 Cov.: 32

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.: 32 AF XY: 0.196 AC XY: 14557 AN XY: 74236

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.204

Alfa AF: 0.190 Hom.: 1799

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	13
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11128951; hg19: chr3-20375546;