rs1520043

Variant names:

• chr3-20477209-T-G
• rs1520043
• ENST00000634618.1:n.1377+95909T>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+95909T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.04 in 152,248 control chromosomes in the GnomAD database, including 329 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 0.040 (329 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 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+95909T>G		intron_variant	Intron 10 of 16	5

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6069 AN: 152128 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0960

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0400 AC: 6088 AN: 152248 Hom.: 329 Cov.: 32 AF XY: 0.0463 AC XY: 3448 AN XY: 74446

African (AFR) AF: 0.0170 AC: 708 AN: 41566

American (AMR) AF: 0.0962 AC: 1470 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1197 AN: 5174

South Asian (SAS) AF: 0.117 AC: 562 AN: 4820

European-Finnish (FIN) AF: 0.0752 AC: 797 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0176 AC: 1199 AN: 68012

Other (OTH) AF: 0.0445 AC: 94 AN: 2110

Alfa AF: 0.0260 Hom.: 584

Bravo AF: 0.0401

Asia WGS AF: 0.172 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.40
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs1520043; hg19: chr3-20518701;