3-181593779-C-T

Variant names:

• chr3-181593779-C-T
• rs9839776
• ENST00000491282.6:n.239-17082C>T

Variant summary

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

The ENST00000491282.6(SOX2-OT):​n.239-17082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,962 control chromosomes in the GnomAD database, including 7,128 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 0.30 (7128 hom., cov: 32)
• Consequence: SOX2-OT ENST00000491282.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 22 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]

ENSG00000239381 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX2-OT	NR_075091.1	n.428-17082C>T		intron_variant	Intron 4 of 7
SOX2-OT	NR_075092.1	n.428-17082C>T		intron_variant	Intron 4 of 6
SOX2-OT	NR_075093.1	n.404-17082C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000491282.6	n.239-17082C>T		intron_variant	Intron 2 of 4	1
SOX2-OT	ENST00000498731.6	n.182-17078C>T		intron_variant	Intron 1 of 4	1
SOX2-OT	ENST00000460739.6	n.422+29851C>T		intron_variant	Intron 4 of 5	4

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45431 AN: 151844 Hom.: 7134 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.299 AC: 45433 AN: 151962 Hom.: 7128 Cov.: 32 AF XY: 0.295 AC XY: 21869 AN XY: 74256

African (AFR) AF: 0.374 AC: 15516 AN: 41442

American (AMR) AF: 0.301 AC: 4595 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3464

East Asian (EAS) AF: 0.185 AC: 952 AN: 5158

South Asian (SAS) AF: 0.169 AC: 814 AN: 4822

European-Finnish (FIN) AF: 0.252 AC: 2660 AN: 10536

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18915 AN: 67958

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.278 Hom.: 4419

Bravo AF: 0.308

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.65
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs9839776; hg19: chr3-181311567;