ENST00000460739.6:n.213+129937C>T

Variant names:

• chr3-181305520-C-T
• rs7651166
• ENST00000460739.6:n.213+129937C>T

Variant summary

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

The ENST00000460739.6(SOX2-OT):​n.213+129937C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,112 control chromosomes in the GnomAD database, including 1,684 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 0.093 (1684 hom., cov: 32)
• Consequence: SOX2-OT ENST00000460739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX2-OT	NR_075091.1	n.218+129937C>T		intron_variant	Intron 3 of 7
SOX2-OT	NR_075092.1	n.218+129937C>T		intron_variant	Intron 3 of 6
SOX2-OT	NR_075093.1	n.194+129937C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX2-OT	ENST00000460739.6	n.213+129937C>T		intron_variant	Intron 3 of 5	4
SOX2-OT	ENST00000469278.5	n.194+129937C>T		intron_variant	Intron 2 of 4	4
SOX2-OT	ENST00000493116.6	n.333+129937C>T		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14112 AN: 151994 Hom.: 1681 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.00686

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0930 AC: 14139 AN: 152112 Hom.: 1684 Cov.: 32 AF XY: 0.0926 AC XY: 6889 AN XY: 74380

African (AFR) AF: 0.276 AC: 11418 AN: 41428

American (AMR) AF: 0.0463 AC: 708 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3470

East Asian (EAS) AF: 0.144 AC: 742 AN: 5144

South Asian (SAS) AF: 0.107 AC: 515 AN: 4816

European-Finnish (FIN) AF: 0.00198 AC: 21 AN: 10616

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.00687 AC: 467 AN: 68024

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.0456 Hom.: 1350

Bravo AF: 0.104

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.52
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7651166; hg19: chr3-181023308;