3-20748689-T-C

Variant names:

• chr3-20748689-T-C
• rs4857969
• ENST00000634618.1:n.1438+49244T>C

Variant summary

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

The ENST00000634618.1(SGO1-AS1):​n.1438+49244T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,886 control chromosomes in the GnomAD database, including 27,166 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 0.60 (27166 hom., cov: 32)
• Consequence: SGO1-AS1 ENST00000634618.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 0 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634618.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGO1-AS1	ENST00000634618.1	TSL:5	n.1438+49244T>C		intron	N/A
	SGO1-AS1	ENST00000634837.1	TSL:5	n.117+16189T>C		intron	N/A
	SGO1-AS1	ENST00000754069.1		n.62-40590T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90429 AN: 151768 Hom.: 27140 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.596 AC: 90504 AN: 151886 Hom.: 27166 Cov.: 32 AF XY: 0.600 AC XY: 44555 AN XY: 74228

African (AFR) AF: 0.576 AC: 23858 AN: 41422

American (AMR) AF: 0.540 AC: 8249 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1857 AN: 3466

East Asian (EAS) AF: 0.603 AC: 3112 AN: 5160

South Asian (SAS) AF: 0.640 AC: 3083 AN: 4818

European-Finnish (FIN) AF: 0.706 AC: 7444 AN: 10548

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.604 AC: 41019 AN: 67884

Other (OTH) AF: 0.575 AC: 1209 AN: 2104

Alfa AF: 0.585 Hom.: 55923

Bravo AF: 0.576

Asia WGS AF: 0.643 AC: 2232 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.44
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs4857969; hg19: chr3-20790181;