chr3-20528881-T-G

Variant names:

• chr3-20528881-T-G
• rs1403651
• ENST00000634618.1:n.1377+147581T>G

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+147581T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,262 control chromosomes in the GnomAD database, including 2,645 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 0.14 (2645 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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+147581T>G		intron_variant	Intron 10 of 16	5

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20908 AN: 152144 Hom.: 2638 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0273

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.138 AC: 20939 AN: 152262 Hom.: 2645 Cov.: 32 AF XY: 0.138 AC XY: 10269 AN XY: 74468

African (AFR) AF: 0.320 AC: 13271 AN: 41522

American (AMR) AF: 0.140 AC: 2147 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3472

East Asian (EAS) AF: 0.174 AC: 897 AN: 5170

South Asian (SAS) AF: 0.240 AC: 1161 AN: 4832

European-Finnish (FIN) AF: 0.0273 AC: 290 AN: 10622

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0404 AC: 2747 AN: 68030

Other (OTH) AF: 0.125 AC: 265 AN: 2116

Alfa AF: 0.0585 Hom.: 847

Bravo AF: 0.153

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.86
DANN	Benign	0.71
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1403651; hg19: chr3-20570373;