chr3-20858640-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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.1727+10357G>C		intron_variant	Intron 14 of 16	5
SGO1-AS1	ENST00000634837.1	n.118-11649G>C		intron_variant	Intron 1 of 7	5

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

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.0787

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0806

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.114

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1498991; hg19: chr3-20900132;