3-20535981-C-T

Variant names:

• chr3-20535981-C-T
• rs1523351
• ENST00000634618.1:n.1377+154681C>T

Variant summary

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

The ENST00000634618.1(SGO1-AS1):​n.1377+154681C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,374 control chromosomes in the GnomAD database, including 9,704 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 0.35 (9704 hom., cov: 29)
• Consequence: SGO1-AS1 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.391 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.1377+154681C>T		intron_variant	Intron 10 of 16	5

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53099 AN: 151256 Hom.: 9698 Cov.: 29

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.351 AC: 53127 AN: 151374 Hom.: 9704 Cov.: 29 AF XY: 0.346 AC XY: 25569 AN XY: 73918

African (AFR) AF: 0.347 AC: 14279 AN: 41192

American (AMR) AF: 0.399 AC: 6063 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1014 AN: 3470

East Asian (EAS) AF: 0.100 AC: 514 AN: 5128

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4810

European-Finnish (FIN) AF: 0.293 AC: 3042 AN: 10388

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.381 AC: 25866 AN: 67886

Other (OTH) AF: 0.313 AC: 658 AN: 2102

Alfa AF: 0.362 Hom.: 14614

Bravo AF: 0.353

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.47
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1523351; hg19: chr3-20577473;