rs11128951

chr3-20334054-A-G

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.571-11606A>G		intron_variant, non_coding_transcript_variant		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;