ENST00000634618.1:n.1727+10357G>C

Variant names:

• chr3-20858640-G-C
• rs1498991
• ENST00000634618.1:n.1727+10357G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000634618.1(SGO1-AS1):​n.1727+10357G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,162 control chromosomes in the GnomAD database, including 1,578 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 0.11 (1578 hom., cov: 33)
• Consequence: SGO1-AS1 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.381 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.1727+10357G>C		intron	N/A
	SGO1-AS1	ENST00000634837.1	TSL:5	n.118-11649G>C		intron	N/A
	SGO1-AS1	ENST00000837212.1		n.91-11649G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16532 AN: 152044 Hom.: 1573 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0806

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.109 AC: 16560 AN: 152162 Hom.: 1578 Cov.: 33 AF XY: 0.115 AC XY: 8531 AN XY: 74396

African (AFR) AF: 0.106 AC: 4419 AN: 41520

American (AMR) AF: 0.254 AC: 3875 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2042 AN: 5162

South Asian (SAS) AF: 0.133 AC: 642 AN: 4818

European-Finnish (FIN) AF: 0.0806 AC: 854 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4149 AN: 67998

Other (OTH) AF: 0.114 AC: 241 AN: 2110

Alfa AF: 0.0282 Hom.: 18

Bravo AF: 0.128

Asia WGS AF: 0.255 AC: 884 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1498991; hg19: chr3-20900132;