rs1558797

chr3-181749102-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000626948.3(SOX2-OT):n.945-25159A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,086 control chromosomes in the GnomAD database, including 13,920 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 (13920 hom., cov: 33)
• Consequence: SOX2-OT ENST00000626948.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOX2-OT	ENST00000626948.3	n.945-25159A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64122 AN: 151968 Hom.: 13909 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.422 AC: 64183 AN: 152086 Hom.: 13920 Cov.: 33 AF XY: 0.427 AC XY: 31727 AN XY: 74336

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.381

Alfa AF: 0.390 Hom.: 1959

Bravo AF: 0.428

Asia WGS AF: 0.462 AC: 1607 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	0.32
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558797; hg19: chr3-181466890;