rs1520043

Positions:

• chr3-20477209-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634618.1(SGO1-AS1):​n.1377+95909T>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.1377+95909T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0170

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0752

Gnomad4 NFE AF: 0.0176

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0239 Hom.: 206

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1520043; hg19: chr3-20518701;