rs1518933

Variant names:

• chr3-181337590-G-A
• rs1518933
• ENST00000460739.6:n.213+162007G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-181337590-G-A
• chr3-181337590-G-C

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+162007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,014 control chromosomes in the GnomAD database, including 15,424 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 0.42 (15424 hom., cov: 32)
• Consequence: SOX2-OT ENST00000460739.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 4 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]

ENSG00000241231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX2-OT	NR_075091.1	n.218+162007G>A		intron_variant	Intron 3 of 7
SOX2-OT	NR_075092.1	n.218+162007G>A		intron_variant	Intron 3 of 6
SOX2-OT	NR_075093.1	n.194+162007G>A		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+162007G>A		intron_variant	Intron 3 of 5	4
SOX2-OT	ENST00000469278.5	n.194+162007G>A		intron_variant	Intron 2 of 4	4
SOX2-OT	ENST00000493116.6	n.333+162007G>A		intron_variant	Intron 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64318 AN: 151896 Hom.: 15418 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.423 AC: 64337 AN: 152014 Hom.: 15424 Cov.: 32 AF XY: 0.426 AC XY: 31673 AN XY: 74320

African (AFR) AF: 0.205 AC: 8523 AN: 41496

American (AMR) AF: 0.424 AC: 6461 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1629 AN: 3466

East Asian (EAS) AF: 0.363 AC: 1876 AN: 5170

South Asian (SAS) AF: 0.376 AC: 1814 AN: 4824

European-Finnish (FIN) AF: 0.627 AC: 6623 AN: 10566

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36140 AN: 67946

Other (OTH) AF: 0.421 AC: 887 AN: 2106

Alfa AF: 0.486 Hom.: 49098

Bravo AF: 0.396

Asia WGS AF: 0.361 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.61
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1518933; hg19: chr3-181055378;