rs1558797

Variant names:

• chr3-181749102-A-G
• rs1558797
• ENST00000498226.6:n.289-41571A>G

Variant summary

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

The ENST00000498226.6(SOX2-OT):​n.289-41571A>G variant causes a intron 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 ENST00000498226.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498226.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	ENST00000498226.6	TSL:4	n.289-41571A>G		intron	N/A
	SOX2-OT	ENST00000593330.2	TSL:3	n.355+49219A>G		intron	N/A
	SOX2-OT	ENST00000595084.3	TSL:5	n.286+49219A>G		intron	N/A

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

African (AFR) AF: 0.506 AC: 20971 AN: 41474

American (AMR) AF: 0.444 AC: 6786 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2626 AN: 5174

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4816

European-Finnish (FIN) AF: 0.483 AC: 5102 AN: 10556

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24682 AN: 67990

Other (OTH) AF: 0.381 AC: 805 AN: 2114

Alfa AF: 0.395 Hom.: 4072

Bravo AF: 0.428

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.42
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1558797; hg19: chr3-181466890;