rs1395103

Variant names:

• chr3-20573781-G-A
• rs1395103
• ENST00000634618.1:n.1378-125604G>A

Variant summary

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

The ENST00000634618.1(SGO1-AS1):​n.1378-125604G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,934 control chromosomes in the GnomAD database, including 5,403 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 0.26 (5403 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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.1378-125604G>A		intron_variant	Intron 10 of 16	5

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39481 AN: 151816 Hom.: 5401 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.260 AC: 39493 AN: 151934 Hom.: 5403 Cov.: 32 AF XY: 0.260 AC XY: 19334 AN XY: 74242

African (AFR) AF: 0.191 AC: 7916 AN: 41470

American (AMR) AF: 0.229 AC: 3494 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3464

East Asian (EAS) AF: 0.262 AC: 1345 AN: 5142

South Asian (SAS) AF: 0.261 AC: 1255 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3490 AN: 10530

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20135 AN: 67946

Other (OTH) AF: 0.273 AC: 575 AN: 2104

Alfa AF: 0.264 Hom.: 4384

Bravo AF: 0.250

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.9
DANN	Benign	0.70
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1395103; hg19: chr3-20615273;