3-20535981-C-T

Position:

• chr3-20535981-C-T

Variant summary

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

The ENST00000634618.1(SGO1-AS1):​n.1377+154681C>T 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 0.351 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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=-0.91).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGO1-AS1	ENST00000634618.1	n.1377+154681C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.313

Alfa AF: 0.360 Hom.: 11685

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1523351; hg19: chr3-20577473;