3-20916359-A-G

Variant names:

• chr3-20916359-A-G
• rs6776153
• ENST00000634837.1:n.261+10752A>G

Variant summary

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

The ENST00000634837.1(SGO1-AS1):​n.261+10752A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,074 control chromosomes in the GnomAD database, including 21,666 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 0.52 (21666 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000634837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 5 publications found

Genes affected

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

LOC107986068 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634837.1. 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	ENST00000634837.1	TSL:5	n.261+10752A>G		intron	N/A
	SGO1-AS1	ENST00000826894.1		n.73+10752A>G		intron	N/A
	SGO1-AS1	ENST00000826895.1		n.73+10752A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78838 AN: 151956 Hom.: 21628 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.499

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.519 AC: 78927 AN: 152074 Hom.: 21666 Cov.: 32 AF XY: 0.516 AC XY: 38329 AN XY: 74336

African (AFR) AF: 0.685 AC: 28396 AN: 41466

American (AMR) AF: 0.443 AC: 6759 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1705 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3355 AN: 5164

South Asian (SAS) AF: 0.679 AC: 3276 AN: 4822

European-Finnish (FIN) AF: 0.361 AC: 3820 AN: 10580

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30069 AN: 67990

Other (OTH) AF: 0.498 AC: 1049 AN: 2108

Alfa AF: 0.456 Hom.: 15085

Bravo AF: 0.528

Asia WGS AF: 0.607 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.99
DANN	Benign	0.74
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs6776153; hg19: chr3-20957851;