3-20747383-C-T

Variant names:

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

Variant summary

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

The ENST00000634618.1(SGO1-AS1):​n.1438+47938C>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 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 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.1438+47938C>T		intron_variant	Intron 11 of 16	5
SGO1-AS1	ENST00000634837.1	n.117+14883C>T		intron_variant	Intron 1 of 7	5

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

Gnomad4 AFR AF: 0.0369

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0408

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0752 Hom.: 618

Bravo AF: 0.0810

Asia WGS AF: 0.251 AC: 871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964910; hg19: chr3-20788875;