ENST00000634618.1:n.571-11606A>G

Variant names:

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

Variant summary

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

The ENST00000634618.1(SGO1-AS1):​n.571-11606A>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
• Publications: 8 publications found

Genes affected

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

ENSG00000296099 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.571-11606A>G		intron	N/A
	SGO1-AS1	ENST00000736217.1		n.329-47121A>G		intron	N/A
	SGO1-AS1	ENST00000736218.1		n.275-47121A>G		intron	N/A

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

African (AFR) AF: 0.148 AC: 6130 AN: 41404

American (AMR) AF: 0.237 AC: 3618 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3466

East Asian (EAS) AF: 0.347 AC: 1794 AN: 5164

South Asian (SAS) AF: 0.239 AC: 1149 AN: 4810

European-Finnish (FIN) AF: 0.198 AC: 2091 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13494 AN: 67928

Other (OTH) AF: 0.204 AC: 431 AN: 2108

Alfa AF: 0.190 Hom.: 2342

Bravo AF: 0.195

Asia WGS AF: 0.275 AC: 950 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs11128951; hg19: chr3-20375546;