rs1158707

Variant names:

• chr3-181503551-A-G
• rs1158707
• ENST00000460739.6:n.214-60169A>G

Variant summary

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

The ENST00000493521.5(SOX2-OT):​n.219-60169A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,114 control chromosomes in the GnomAD database, including 10,864 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 0.34 (10864 hom., cov: 32)
• Consequence: SOX2-OT ENST00000493521.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 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]

ENSG00000294823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493521.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	NR_075091.1		n.219-60169A>G		intron	N/A
	SOX2-OT	NR_075092.1		n.219-60169A>G		intron	N/A
	SOX2-OT	NR_075093.1		n.195-60169A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOX2-OT	ENST00000460739.6	TSL:4	n.214-60169A>G		intron	N/A
	SOX2-OT	ENST00000469278.5	TSL:4	n.195-60169A>G		intron	N/A
	SOX2-OT	ENST00000493116.6	TSL:4	n.334-60169A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51859 AN: 151998 Hom.: 10866 Cov.: 32

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.341 AC: 51860 AN: 152114 Hom.: 10864 Cov.: 32 AF XY: 0.343 AC XY: 25514 AN XY: 74362

African (AFR) AF: 0.0891 AC: 3702 AN: 41546

American (AMR) AF: 0.390 AC: 5967 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2046 AN: 5166

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4820

European-Finnish (FIN) AF: 0.483 AC: 5094 AN: 10552

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31033 AN: 67960

Other (OTH) AF: 0.334 AC: 705 AN: 2112

Alfa AF: 0.403 Hom.: 1766

Bravo AF: 0.327

Asia WGS AF: 0.322 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.63
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1158707;

hg19: chr3-181221339;