3-20747383-C-T

Variant names:

• chr3-20747383-C-T
• rs964910
• ENST00000634618.1:n.1438+47938C>T

Variant summary

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

The ENST00000754069.1(SGO1-AS1):​n.62-41896C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,112 control chromosomes in the GnomAD database, including 744 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 0.077 (744 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000754069.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754069.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGO1-AS1	ENST00000634618.1	TSL:5	n.1438+47938C>T		intron	N/A
	SGO1-AS1	ENST00000634837.1	TSL:5	n.117+14883C>T		intron	N/A
	SGO1-AS1	ENST00000754069.1		n.62-41896C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11728 AN: 151994 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0370

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0408

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.0927

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

GnomAD4 genome AF: 0.0771 AC: 11735 AN: 152112 Hom.: 744 Cov.: 32 AF XY: 0.0801 AC XY: 5957 AN XY: 74364

African (AFR) AF: 0.0369 AC: 1533 AN: 41500

American (AMR) AF: 0.126 AC: 1928 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0430 AC: 149 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1800 AN: 5154

South Asian (SAS) AF: 0.138 AC: 666 AN: 4820

European-Finnish (FIN) AF: 0.0408 AC: 432 AN: 10582

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0726 AC: 4937 AN: 67986

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0744 Hom.: 767

Bravo AF: 0.0810

Asia WGS AF: 0.251 AC: 871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.80
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs964910; hg19: chr3-20788875;