3-181486314-G-T

Variant names:

• chr3-181486314-G-T
• rs2199718
• ENST00000725558.1:n.49G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000725558.1(SOX2-OT):​n.49G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,310 control chromosomes in the GnomAD database, including 15,397 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 0.43 (15397 hom., cov: 30)
• Consequence: SOX2-OT ENST00000725558.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 2 publications found

Genes affected

SOX2-OT (HGNC:20209): (SOX2 overlapping transcript) This gene produces alternatively spliced long non-coding RNAs. These RNAs were observed to be upregulated in tumor cells and positively correlated to expression of the SRY-box 2 gene. Overexpression of these transcripts may promote cell proliferation. [provided by RefSeq, Dec 2017]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725558.1. 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
	SOX2-OT	NR_075091.1		n.219-77406G>T		intron	N/A
	SOX2-OT	NR_075092.1		n.219-77406G>T		intron	N/A
	SOX2-OT	NR_075093.1		n.195-77406G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	ENST00000725558.1		n.49G>T		non_coding_transcript_exon	Exon 1 of 4
	SOX2-OT	ENST00000460739.6	TSL:4	n.214-77406G>T		intron	N/A
	SOX2-OT	ENST00000469278.5	TSL:4	n.195-77406G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65691 AN: 151190 Hom.: 15383 Cov.: 30

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.434 AC: 65725 AN: 151310 Hom.: 15397 Cov.: 30 AF XY: 0.435 AC XY: 32149 AN XY: 73864

African (AFR) AF: 0.249 AC: 10281 AN: 41208

American (AMR) AF: 0.509 AC: 7741 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1570 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2302 AN: 5108

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4812

European-Finnish (FIN) AF: 0.525 AC: 5434 AN: 10352

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.515 AC: 34974 AN: 67850

Other (OTH) AF: 0.434 AC: 914 AN: 2108

Alfa AF: 0.476 Hom.: 27090

Bravo AF: 0.421

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	5.7
DANN	Benign	0.71
PhyloP100		0.030

Splicing

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

Other links and lift over

dbSNP: rs2199718; hg19: chr3-181204102;